Research Computing Center Wiki - User contributions [en]

RevBayes-Teaching

2019-01-09T16:17:46Z

Yhuang: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.0.10 ===..."

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
1.0.10

=== Author / Distributor ===

[https://github.com/revbayes/revbayes RevBayes]

=== Description ===
"
Bayesian phylogenetic inference using probabilistic graphical models and an interactive language."
More details are at [https://github.com/revbayes/revbayes RevBayes]

=== Running Program ===

The last version of this application is at /usr/local/apps/gb/RevBayes/1.0.10

To use this version, please load the module with
<pre class="gscript">
ml RevBayes/1.0.10
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_RevBayes 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=RevBayes.%j.out 
<nowiki>#</nowiki>SBATCH --error=RevBayes.%j.err 

cd $SLURM_SUBMIT_DIR 
ml RevBayes/1.0.10 
rb [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml RevBayes/1.0.10
rb -h
Usage: rb [OPTIONS]
rb [OPTIONS] <file1> [<file2> ...]
Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language

Options:
-h [ --help ] Show information on flags.
-v [ --version ] Show version and exit.
-b [ --batch ] Run in batch mode.
--file arg File(s) to source.
--setOption arg Set an option key=value.

See http://revbayes.github.io for more information
</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://github.com/revbayes/revbayes/releases RevBayes]

=== System ===
64-bit Linux

Systems

2018-12-09T02:09:26Z

Yhuang: /* Software Installed on the teaching cluster */

[[Category:Sapelo2]]
[[Category:Teaching]]



=== Sapelo2 ===

Sapelo2 is a Linux cluster that runs a 64-bit CentOS 7.5 operating system and it is managed using Foreman and Puppet. Two physical login nodes are available, with Intel Xeon E5-2680 v3 (Haswell) processors and 128GB of RAM and 24 cores per node.

For a subset of compute nodes, internodal communication among them and between these nodes and the storage systems serving the home directories and the scratch directories is provided by a QDR Infiniband network(40Gbps). For another subset of compute nodes, these communications are provided by an EDR Infiniband network.

The cluster is currently comprised of the following resources:

*42 compute nodes with Intel Xeon Skylake processors (32 cores and 187GB of RAM per node)
*76 compute nodes with AMD Opteron processors (48 cores and 128GB of RAM per node)
*30 compute nodes with Intel Xeon Broadwell processors (28 cores and 64GB of RAM per node)
* 4 compute nodes with AMD Opteron processors (48 cores and 256GB of RAM per node)
* 4 compute node with Intel Xeon processors (28 cores and 1TB of RAM per node)
* 1 compute node with AMD Opteron processors (48 cores and 1TB of RAM per node)
* 4 compute nodes with AMD Opteron processors (48 cores and 512GB of RAM per node)
* 1 compute node with Intel Xeon processors (32 cores and 512GB of RAM per node)
* 4 compute nodes with Intel Xeon Skylake processors (32 cores and 187GB of RAM) and 1 NVIDIA P100 GPU card per node
* 2 compute nodes with Intel Xeon processors (16 cores and 128GB of RAM) and 7 NVIDIA K40m GPU cards per node
* 4 compute nodes with Intel Xeon processors (12 cores and 96GB of RAM) and 7 NVIDIA K20Xm GPU cards per node
* buyin nodes

'''Notes'''

<blockquote style="background-color: lightyellow; border: solid thin grey;">
Your home directory and /lustre1 directory on Sapelo2 are the same as on Sapelo. Therefore, there is no need to transfer data between your Sapelo and Sapelo2 home directories and /lustre1 directories.
</blockquote>

The queueing system on Sapelo2 is Torque/Moab.

====[[Sapelo2 Frequently Asked Questions]]====

====[[Sapelo and Sapelo2 comparison]]====

====[[Connecting#Connecting_to_Sapelo2 |Connecting to Sapelo2]]====

====[[Transferring Files]]====

====[[Disk Storage]]====

====[[Software Installed on Sapelo2]]====

====[[Code Compilation on Sapelo2]]====

====[[Running Jobs on Sapelo2]]====

====[[Monitoring Jobs on Sapelo2]]====

----
[[#top|Back to Top]]

=== Teaching cluster ===

The teaching cluster is a Linux cluster that runs a 64-bit Linux, with Centos 7.5. The physical login node has two 6-core Intel Xeon E5-2620 processors and 128GB of RAM and it runs Red Hat EL 7.5. An Ethernet network (1Gbps) provides internodal communication among compute nodes, and between the compute nodes and the storage systems serving the home directories and the work directories.

The cluster is currently comprised of the following resources:

*37 compute nodes with Intel Xeon X5650 2.67GHz processors (12 cores and 48GB of RAM per node)
* 2 compute nodes with Intel Xeon E5504 2.00GHz processors (8 cores and 48GB of RAM per node)
* 3 compute nodes with Intel Xeon E5504 2.00GHz processors (8 cores and 192GB of RAM per node)
* 2 compute nodes with AMD Opteron 6174 processors (48 cores and 128GB of RAM per node)
* 3 compute nodes with AMD Opteron 6128 HE 2.00GHz processors (32 cores and 64GB of RAM per node)
* 6 NVIDIA Tesla (Fermi) M2070 GPU cards (8 x 448 = 3584 GPU cores). These cards are installed on one host that has dual 6-core Intel Xeon CPUs and 48GB of RAM

The queueing system on the teaching cluster is Slurm.

====[[Connecting#Connecting_to_the_teaching_cluster |Connecting to the teaching cluster]]====

====[[Transferring Files]]====

====[[Disk Storage]]====

====Software Installed on the teaching cluster====

The list of installed application is available at [[Software]] page.

====[[Code Compilation on the teaching cluster]]====

====[[Running Jobs on the teaching cluster]]====

====[[Monitoring Jobs on the teaching cluster]]====

Systems

2018-12-09T02:08:49Z

Yhuang: /* Software Installed on the teaching cluster */

[[Category:Sapelo2]]
[[Category:Teaching]]



=== Sapelo2 ===

Sapelo2 is a Linux cluster that runs a 64-bit CentOS 7.5 operating system and it is managed using Foreman and Puppet. Two physical login nodes are available, with Intel Xeon E5-2680 v3 (Haswell) processors and 128GB of RAM and 24 cores per node.

For a subset of compute nodes, internodal communication among them and between these nodes and the storage systems serving the home directories and the scratch directories is provided by a QDR Infiniband network(40Gbps). For another subset of compute nodes, these communications are provided by an EDR Infiniband network.

The cluster is currently comprised of the following resources:

*42 compute nodes with Intel Xeon Skylake processors (32 cores and 187GB of RAM per node)
*76 compute nodes with AMD Opteron processors (48 cores and 128GB of RAM per node)
*30 compute nodes with Intel Xeon Broadwell processors (28 cores and 64GB of RAM per node)
* 4 compute nodes with AMD Opteron processors (48 cores and 256GB of RAM per node)
* 4 compute node with Intel Xeon processors (28 cores and 1TB of RAM per node)
* 1 compute node with AMD Opteron processors (48 cores and 1TB of RAM per node)
* 4 compute nodes with AMD Opteron processors (48 cores and 512GB of RAM per node)
* 1 compute node with Intel Xeon processors (32 cores and 512GB of RAM per node)
* 4 compute nodes with Intel Xeon Skylake processors (32 cores and 187GB of RAM) and 1 NVIDIA P100 GPU card per node
* 2 compute nodes with Intel Xeon processors (16 cores and 128GB of RAM) and 7 NVIDIA K40m GPU cards per node
* 4 compute nodes with Intel Xeon processors (12 cores and 96GB of RAM) and 7 NVIDIA K20Xm GPU cards per node
* buyin nodes

'''Notes'''

<blockquote style="background-color: lightyellow; border: solid thin grey;">
Your home directory and /lustre1 directory on Sapelo2 are the same as on Sapelo. Therefore, there is no need to transfer data between your Sapelo and Sapelo2 home directories and /lustre1 directories.
</blockquote>

The queueing system on Sapelo2 is Torque/Moab.

====[[Sapelo2 Frequently Asked Questions]]====

====[[Sapelo and Sapelo2 comparison]]====

====[[Connecting#Connecting_to_Sapelo2 |Connecting to Sapelo2]]====

====[[Transferring Files]]====

====[[Disk Storage]]====

====[[Software Installed on Sapelo2]]====

====[[Code Compilation on Sapelo2]]====

====[[Running Jobs on Sapelo2]]====

====[[Monitoring Jobs on Sapelo2]]====

----
[[#top|Back to Top]]

=== Teaching cluster ===

The teaching cluster is a Linux cluster that runs a 64-bit Linux, with Centos 7.5. The physical login node has two 6-core Intel Xeon E5-2620 processors and 128GB of RAM and it runs Red Hat EL 7.5. An Ethernet network (1Gbps) provides internodal communication among compute nodes, and between the compute nodes and the storage systems serving the home directories and the work directories.

The cluster is currently comprised of the following resources:

*37 compute nodes with Intel Xeon X5650 2.67GHz processors (12 cores and 48GB of RAM per node)
* 2 compute nodes with Intel Xeon E5504 2.00GHz processors (8 cores and 48GB of RAM per node)
* 3 compute nodes with Intel Xeon E5504 2.00GHz processors (8 cores and 192GB of RAM per node)
* 2 compute nodes with AMD Opteron 6174 processors (48 cores and 128GB of RAM per node)
* 3 compute nodes with AMD Opteron 6128 HE 2.00GHz processors (32 cores and 64GB of RAM per node)
* 6 NVIDIA Tesla (Fermi) M2070 GPU cards (8 x 448 = 3584 GPU cores). These cards are installed on one host that has dual 6-core Intel Xeon CPUs and 48GB of RAM

The queueing system on the teaching cluster is Slurm.

====[[Connecting#Connecting_to_the_teaching_cluster |Connecting to the teaching cluster]]====

====[[Transferring Files]]====

====[[Disk Storage]]====

====[[Software Installed on the teaching cluster]]====

The list of installed application is available at [[Software]] page.

====[[Code Compilation on the teaching cluster]]====

====[[Running Jobs on the teaching cluster]]====

====[[Monitoring Jobs on the teaching cluster]]====

Connecting

2018-11-26T16:15:12Z

Yhuang:

[[Category:Sapelo2]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Please refer to below on "log in to teach via SSH Secure Shell on Windows."

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN].

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 5.png|600px]]

[[File:Teach login 6.png|600px]]

[[File:Teach login 0.png|600px]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png|400px]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-26T16:09:12Z

Yhuang: /* Connecting to the teaching cluster */

[[Category:Sapelo2]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN].

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 5.png|600px]]

[[File:Teach login 6.png|600px]]

[[File:Teach login 0.png|600px]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png|400px]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-26T16:08:03Z

Yhuang: /* Open a connection to the teaching cluster on campus */

[[Category:Sapelo2]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN].

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 0.png|400px]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png|400px]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

5. If above steps fail, please make sure the "keyboard interactive" is in place

[[File:Teach login 5.png|600px]]

[[File:Teach login 6.png|600px]]

[[File:Teach login 7.png|600px]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-26T16:07:31Z

Yhuang: /* Open a connection to the teaching cluster on campus */

[[Category:Sapelo2]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN].

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 0.png|400px]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png|400px]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

5. If above steps fail, please make sure the "keyboard interactive" is in place

[[File:Teach login 5.png|400px]]

[[File:Teach login 6.png|400px]]

[[File:Teach login 7.png|400px]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Bioinformatics Databases

2018-11-26T15:56:26Z

Yhuang:

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members, in the commonly shared "/db" filesystem.

Of the public local databases in /db, NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every other month in fasta format. From these updated datasets, we will also build NCBI Blast and WUBlast databases in both nucleotide and protein formats.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.

For datasets requested by individual lab groups, GACRC staff will assist in setting up a group-shared environment and request that group members maintain their database files there.

For datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Cluster
|-
| [[Bacteria NCBI-sapelo2|Bacteria NCBI]] || 12/21/2017 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[gss-Sapelo2|gss]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[htgs-Sapelo2|htgs]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[hg19-Sapelo2 | hg]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Database]] || every other month || [[:Category:Sapelo2|Sapelo2]]
|-
| [[NCBI Fasta-Sapelo2|NCBI Fasta]] || every other month || [[:Category:Sapelo2|Sapelo2]]
|-
| [[PfamDB-Sapelo2|pfam]] || 27.0 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Refseq-Sapelo2|Refseq]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[TaxDB-Sapelo2|TaxDB]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Uniprot-Sapelo2|Uniprot]] || 06/28/2018 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Uniref-Sapelo2|Uniref]] || 06/28/2018 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[wublast-Sapelo2|wublast]] || || [[:Category:Sapelo2|Sapelo2]]
|-
|}

Bioinformatics Databases

2018-11-19T18:31:00Z

Yhuang:

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members, in the commonly shared "/db" filesystem.

Of the public local databases in /db, NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every other month in fasta format. From these updated datasets, we will also build NCBI Blast and WUBlast databases in both nucleotide and protein formats.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.

For datasets requested by individual lab groups, GACRC staff will assist in setting up a group-shared environment and request that group members maintain their database files there.

For datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Cluster
|-
| [[Bacteria NCBI]] || 12/21/2017 || [[:Category:Sapelo|Sapelo]]
|-
| [[Bacteria NCBI-sapelo2|Bacteria NCBI]] || 12/21/2017 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[gss-Sapelo2|gss]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[htgs-Sapelo2|htgs]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[hg19-Sapelo2 | hg]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Database]] || every other month || [[:Category:Sapelo2|Sapelo2]]
|-
| [[NCBI Fasta-Sapelo|NCBI Fasta]] || every other month || [[:Category:Sapelo|Sapelo]]
|-
| [[NCBI Fasta-Sapelo2|NCBI Fasta]] || every other month || [[:Category:Sapelo2|Sapelo2]]
|-
| [[PfamDB-Sapelo2|pfam]] || 27.0 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Refseq-Sapelo2|Refseq]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[TaxDB-Sapelo2|TaxDB]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Uniprot-Sapelo2|Uniprot]] || 06/28/2018 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Uniref-Sapelo2|Uniref]] || 06/28/2018 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[wublast-Sapelo2|wublast]] || || [[:Category:Sapelo2|Sapelo2]]
|-
|}

Bioinformatics Databases

2018-11-19T18:29:05Z

Yhuang:

As part of our services, the GACRC builds and hosts local copies of frequently cited application data, and provides assistance for sharing data among GACRC members, in the commonly shared "/db" filesystem.

Of the public local databases in /db, NCBI's nr and nt datasets are the most commonly used at the GACRC. GACRC staff will update these datasets every other month in fasta format. From these updated datasets, we will also build NCBI Blast and WUBlast databases in both nucleotide and protein formats.

Various subject datasets, e.g. pfam, bowtie indexes of human and mouse, and NCBI bacterial datasets, are hosted as well. These datasets either don’t need updating, the source does not update frequently, or the datasets are not used frequently by our users. These datasets will only be updated by user request.

For datasets requested by individual lab groups, GACRC staff will assist in setting up a group-shared environment and request that group members maintain their database files there.

For datasets frequently updated by their source, the GACRC encourages users to maintain their own copies of these public databases.

The set of data which are regularly updated is open to review, and can be expanded based on available GACRC resources.

==Installed Bioinformatics Databases ==
{| border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable sortable"
|-
! scope="col" | Name
! scope="col" class="unsortable" | Version
! scope="col" | Cluster
|-
| [[Bacteria NCBI]] || 12/21/2017 || [[:Category:Sapelo|Sapelo]]
|-
| [[gss-Sapelo2|gss]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[htgs-Sapelo2|htgs]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[hg19-Sapelo2 | hg]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[BLAST Databases-Sapelo2 | NCBI BLAST Database]] || every other month || [[:Category:Sapelo2|Sapelo2]]
|-
| [[NCBI Fasta-Sapelo|NCBI Fasta]] || every other month || [[:Category:Sapelo|Sapelo]]
|-
| [[PfamDB-Sapelo2|pfam]] || 27.0 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Refseq-Sapelo2|Refseq]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[TaxDB-Sapelo2|TaxDB]] || || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Uniprot-Sapelo2|Uniprot]] || 06/28/2018 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[Uniref-Sapelo2|Uniref]] || 06/28/2018 || [[:Category:Sapelo2|Sapelo2]]
|-
| [[wublast-Sapelo2|wublast]] || || [[:Category:Sapelo2|Sapelo2]]
|-
|}

Connecting

2018-11-15T16:29:55Z

Yhuang: /* Open a connection to the teaching cluster on campus */

[[Category:Sapelo2]][[Category:Sapelo]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to Sapelo==
Access to the Sapelo is through secure shell (ssh) to the host IP address 128.192.75.104 (note that connection via telnet is not safe and it is therefore disabled). If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to host IP address: 128.192.75.104===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to 128.192.75.104, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@128.192.75.104
</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@128.192.75.104
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh 128.192.75.104
</pre>

In order to enable X forwarding from the new cluster to a local '''Mac OS X machine''', the ssh command given above (i.e. ssh -X UGAMyID@128.192.75.104) has to be issued from an '''X11 terminal''' (and not from a regular terminal).

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@128.192.75.104).

Now you can issue commands to start up X applications on 128.192.75.104, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo]] page.

===Logging in===

When your ssh connection is established, you will be prompted for your UGA MyID password.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 0.png|400px]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png|400px]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-15T16:28:51Z

Yhuang: /* Open a connection to the teaching cluster on campus */

[[Category:Sapelo2]][[Category:Sapelo]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to Sapelo==
Access to the Sapelo is through secure shell (ssh) to the host IP address 128.192.75.104 (note that connection via telnet is not safe and it is therefore disabled). If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to host IP address: 128.192.75.104===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to 128.192.75.104, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@128.192.75.104
</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@128.192.75.104
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh 128.192.75.104
</pre>

In order to enable X forwarding from the new cluster to a local '''Mac OS X machine''', the ssh command given above (i.e. ssh -X UGAMyID@128.192.75.104) has to be issued from an '''X11 terminal''' (and not from a regular terminal).

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@128.192.75.104).

Now you can issue commands to start up X applications on 128.192.75.104, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo]] page.

===Logging in===

When your ssh connection is established, you will be prompted for your UGA MyID password.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 0.png]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png|400px]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-15T16:28:15Z

Yhuang:

[[Category:Sapelo2]][[Category:Sapelo]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to Sapelo==
Access to the Sapelo is through secure shell (ssh) to the host IP address 128.192.75.104 (note that connection via telnet is not safe and it is therefore disabled). If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to host IP address: 128.192.75.104===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to 128.192.75.104, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@128.192.75.104
</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@128.192.75.104
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh 128.192.75.104
</pre>

In order to enable X forwarding from the new cluster to a local '''Mac OS X machine''', the ssh command given above (i.e. ssh -X UGAMyID@128.192.75.104) has to be issued from an '''X11 terminal''' (and not from a regular terminal).

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@128.192.75.104).

Now you can issue commands to start up X applications on 128.192.75.104, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo]] page.

===Logging in===

When your ssh connection is established, you will be prompted for your UGA MyID password.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 0.png|200px]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-15T16:25:11Z

Yhuang:

[[Category:Sapelo2]][[Category:Sapelo]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to Sapelo==
Access to the Sapelo is through secure shell (ssh) to the host IP address 128.192.75.104 (note that connection via telnet is not safe and it is therefore disabled). If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to host IP address: 128.192.75.104===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to 128.192.75.104, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@128.192.75.104
</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@128.192.75.104
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh 128.192.75.104
</pre>

In order to enable X forwarding from the new cluster to a local '''Mac OS X machine''', the ssh command given above (i.e. ssh -X UGAMyID@128.192.75.104) has to be issued from an '''X11 terminal''' (and not from a regular terminal).

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@128.192.75.104).

Now you can issue commands to start up X applications on 128.192.75.104, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo]] page.

===Logging in===

When your ssh connection is established, you will be prompted for your UGA MyID password.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''
Here are steps for log in to teach via SSH Secure Shell.

1.

If log in via "Quick Connect", please select the "Keyboard Interactive":

[[File:Teach login 4.png]]

If log in via "Profiles", please select the "Keyboard Interactive":

[[File:Teach login 0.png]]

2. The next step is to fill your password of MyID:

[[File:Teach login 1.png]]

3. fill push in the field to push an Duo Pass request

[[File:Teach login 2.png]]

4. Approve the Authentication request via your device, e.x. mobile phone

5. Finalize the log in by clicking "OK"

[[File:Teach login 3.png]]

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Connecting

2018-11-15T16:10:25Z

Yhuang: /* Connecting to the teaching cluster */

[[Category:Sapelo2]][[Category:Sapelo]][[Category:Teaching]]

==Connecting to Sapelo2==

Access to Sapelo2 requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the Sapelo2 is through secure shell (ssh) to the host sapelo2.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to Sapelo2 on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to Sapelo2, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@sapelo2.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@sapelo2.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh sapelo2.gacrc.uga.edu
</pre>

===Open a connection to Sapelo2 from off-campus===

VPN is needed to connect to Sapelo2 from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to sapelo2.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@sapelo2.gacrc.uga.edu).

Now you can issue commands to start up X applications on sapelo2.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo2]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to Sapelo==
Access to the Sapelo is through secure shell (ssh) to the host IP address 128.192.75.104 (note that connection via telnet is not safe and it is therefore disabled). If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to host IP address: 128.192.75.104===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to 128.192.75.104, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@128.192.75.104
</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@128.192.75.104
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh 128.192.75.104
</pre>

In order to enable X forwarding from the new cluster to a local '''Mac OS X machine''', the ssh command given above (i.e. ssh -X UGAMyID@128.192.75.104) has to be issued from an '''X11 terminal''' (and not from a regular terminal).

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@128.192.75.104).

Now you can issue commands to start up X applications on 128.192.75.104, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on Sapelo]] page.

===Logging in===

When your ssh connection is established, you will be prompted for your UGA MyID password.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

==Connecting to the teaching cluster==

Access to the teaching cluster requires an active MyID and password, and two-factor authentication with Archpass Duo. For more details of Archpass Duo, please refer to
[https://eits.uga.edu/access_and_security/infosec/tools/archpass_duo archpass_duo] .

Access to the teaching cluster is through secure shell (ssh) to the host teach.gacrc.uga.edu . If you have a local system that runs an X Window client or server, you can run X applications remotely.

To connect via ssh, you must have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including Linux and Mac OS X). An SSH Secure Shell Utility is available for Windows on the [https://eits.uga.edu/hardware_and_software/software UGA Sitesoft] page (you will need to enter your UGA myID and password to download the software).

===Open a connection to the teaching cluster on campus===

'''Examples of usage on Unix/Linux/MacOSX'''

To open a connection to the teaching cluster, first open a terminal and at the command prompt type

<pre class="gcommand">
ssh UGAMyID@teach.gacrc.uga.edu

Duo two-factor login for UGAMyID

Enter a passcode or select one of the following options:

1. Duo Push to XXX-XXX-4304
2. Phone call to XXX-XXX-4304
3. SMS passcodes to XXX-XXX-4304

Passcode or option (1-3):

</pre>

or

<pre class="gcommand">
ssh -X UGAMyID@teach.gacrc.uga.edu
</pre>

where '''''UGAMyID''''' is your UGA MyID. The -X option might be necessary to allow X windows applications running on the new cluster to be forwarded to your local machine. If your username on your local system is the same as your UGA MyID, you can simply type

<pre class="gcommand">
ssh teach.gacrc.uga.edu
</pre>

'''Examples of usage on Windows'''

===Open a connection to the teaching cluster from off-campus===

VPN is needed to connect to the teaching cluster from off-campus (outside the UGA main campus).

For connecting from off-campus, please first connect to the UGA VPN and then connect to teach.gacrc.uga.edu. Information on how to use the VPN is available at [https://eits.uga.edu/access_and_security/infosec/tools/vpn/ UGA_VPN]

===To run X Window applications remotely on your local machine===

If you have a local machine that runs an X Window client or server, you can forward X Window applications running on the new cluster to your local machine. Recent releases of Unix based operating systems (including Linux and Mac OS X) come with an X windows client. For Windows OS, a free X windows server is Xming. More information on how to install Xming is available on the [[Frequently Asked Questions | GACRC FAQ]] page.

Your ssh may be configured to allow you to run X Window application on your local machine automatically. If it does not, try including the -X flag when connecting to the new cluster (ssh -X UGAMyID@teach.gacrc.uga.edu).

Now you can issue commands to start up X applications on teach.gacrc.uga.edu, such as xterm.

If you plan to run resource consuming X Window applications, such as graphics programs, etc, please use the queueing system to get a command prompt on an interactive node. Information on how to run interactive jobs on the new cluster is at the [[Running Jobs on the teaching cluster]] page.

===Logging out===

To leave the system, be sure that all your open files are closed and all stopped jobs have been terminated then enter:

<pre class="gcommand">
exit
</pre>

Getting Help

2018-11-14T18:23:20Z

Yhuang:

The primary way to contact us for help and initial consultation is via our support form (see below). You can also call the EITS Help Desk at 706-542-3106 and they will either redirect your call to one of us, or enter a support ticket on your behalf. You are welcome to email or call us directly, but because we aren't always sitting at our desk it is best to use a support form, as that is seen by all GACRC staff who are present at the time.

* On Nov. 14, 2018, we changed our ticketing system to the EITS GACRC TeamDynamix ticketing system. To help us process the tickets more efficiently, the new system has specific entries for different types of support requests.

Here is the GACRC catalog that lists the help forms for the various services that we provide:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC Support Entry]

To request software installation or update, please use this form:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25850 Software Request]

To request general help, please use this form:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support]

This ticketing system requires UGA MyID authentication to be accessed.

'''Office Hours''': GACRC staff are located in the Computing Services Building (formerly called Statistics Building), rooms 101 to 108. Our office is open Monday through Friday from 9am until 5pm. You are welcome to stop by and ask questions, or you can schedule an appointment using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support].

'''Directions''': The Computing Services Building is located at 101 Cedar Street, Athens, GA 30602, on the corner of Cedar Street and East Campus Rd. As you enter the building from the entrance on Cedar Street, on the East Campus Rd. end of the building, there are stairs leading down to the first floor. Our offices are on your left, as you come down those stairs.

Instructional Accounts

2018-11-14T17:00:29Z

Yhuang:

* At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. The registration links in this page are updated to the new pages.

Here is the landing page of all entries for account request:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC Support Entry]

Generic instructional user accounts are available on the Linux cluster for courses that teach high-performance computing methods. Besides the number of accounts needed, we also need to know the course name (e.g., GENE8940) and what type of resources are required (e.g., special queue, large memory, specific applications or data sets, or none). Typical requests are for 10 - 30 user accounts, with a common data directory where the instructor provides data files for the class.

All users of instructional accounts must attend a training session led by one of our instructors, before being given access to GACRC resources. The training session usually takes about an hour, so please plan for that in your class scheduling.

Requests for accounts should be made via the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25840 Class Account Creation] at the beginning of the semester in which the course is taught (i.e., please don't wait until the last minute). Any following changes can be addressed at [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=258410 Class Account Modification]

User Accounts

2018-11-14T17:00:14Z

Yhuang:

* At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. The registration links in this page are updated to the new pages.

Here is the landing page of all entries for account request:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC Support Entry]

All persons using GACRC resources must meet the requirements described on the GACRC [http://gacrc.uga.edu/about/policies Policies] page.

GACRC user accounts are managed as part of a "computing lab" group which is registered by a UGA principal investigator (PI) i.e. faculty member. Users are typically post-docs and graduate students working under the direction of the PI. The account creation process is twofold:

====Computing Lab Registration====

A UGA faculty member may request a computing lab with us by providing the following information on our [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25847 Lab Registration].

Any following changes can be addressed at [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25847 Lab Modification/Deletion]

By applying for a group account, the Principal Investigator is agreeing that all users will abide by the [http://eits.uga.edu/access_and_security/infosec/pols_regs/policies/aup UGA Policies on the Use of Computers].

====User Accounts====

The PI of a computing lab must request user accounts for members of his/her computing lab. Please use our [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 User Accounts Registration].

Any following changes can be addressed at [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25848 Account Modification/Deletion]

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.
'''

User Accounts

2018-11-14T16:57:45Z

Yhuang:

* At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. The registration links in this page are updated to the new pages.

All persons using GACRC resources must meet the requirements described on the GACRC [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 User Account Registration] page.

GACRC user accounts are managed as part of a "computing lab" group which is registered by a UGA principal investigator (PI) i.e. faculty member. Users are typically post-docs and graduate students working under the direction of the PI. The account creation process is twofold:

====Computing Lab Registration====

A UGA faculty member may request a computing lab with us by providing the following information on our [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25847 Lab Registration].

Any following changes can be addressed at [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25847 Lab Modification/Deletion]

By applying for a group account, the Principal Investigator is agreeing that all users will abide by the [http://eits.uga.edu/access_and_security/infosec/pols_regs/policies/aup UGA Policies on the Use of Computers].

====User Accounts====

The PI of a computing lab must request user accounts for members of his/her computing lab. Please use our [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 User Accounts Registration].

Any following changes can be addressed at [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25848 Account Modification/Deletion]

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.
'''

Getting Help

2018-11-14T16:53:01Z

Yhuang:

At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. To facilitate the process of help, the new system has specific entries for different subjects of requests.

Here is the landing page of all entries for help:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC Support Entry]

For requests of software installation or update:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25850 Software Request]

For request of general help:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support]

This ticking system needs MYID to log in.

The primary way to contact us for help and initial consultation is via our support form. You can also call the EITS Help Desk at 542-3106 and they will either redirect your call to one of us, or enter a support ticket on your behalf. You are welcome to email or call us directly, but because we aren't always sitting at our desk it is best to use the form because it is guaranteed to be seen by all who are present at the time.

'''Office Hours''': GACRC staff are located in the Computing Services Building (formerly called Statistics Building), rooms 101 to 108. Our office is open Monday through Friday from 9am until 5pm. You are welcome to stop by and ask questions, or you can schedule an appointment using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support].

'''Directions''': The Computing Services Building is located at 101 Cedar Street, Athens, GA 30602, on the corner of Cedar Street and East Campus Rd. As you enter the building from the entrance on Cedar Street, on the East Campus Rd. end of the building, there are stairs leading down to the first floor. Our offices are on your left, as you come down those stairs.

User Accounts

2018-11-14T16:50:52Z

Yhuang:

* At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. The registration links in this page are updated to the new pages.

All persons using GACRC resources must meet the requirements described on the GACRC [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 User Account Registration] page.

GACRC user accounts are managed as part of a "computing lab" group which is registered by a UGA principal investigator (PI) i.e. faculty member. Users are typically post-docs and graduate students working under the direction of the PI. The account creation process is twofold:

====Computing Lab Registration====

A UGA faculty member may request a computing lab with us by providing the following information on our [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25847 Lab Registration]:

By applying for a group account, the Principal Investigator is agreeing that all users will abide by the [http://eits.uga.edu/access_and_security/infosec/pols_regs/policies/aup UGA Policies on the Use of Computers].

====User Accounts====

The PI of a computing lab must request user accounts for members of his/her computing lab. Please use our [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25839 User Accounts Registration] and provide the following information:

'''NOTE: New users are required to attend an introductory training session and information about that will be sent once an account is requested.
'''

Getting Help

2018-11-14T16:44:52Z

Yhuang:

At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. To facilitate the process of help, the new system has specific entries for different subjects of requests.

Here is the landing page of all entries for help:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC Support Entry]

For requests of troubleshooting:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 Troubleshooting]

For requests of software installation:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 Software Installation]

For request of general help:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC General Support]

This ticking system needs MYID to log in.

The primary way to contact us for help and initial consultation is via our support form. You can also call the EITS Help Desk at 542-3106 and they will either redirect your call to one of us, or enter a support ticket on your behalf. You are welcome to email or call us directly, but because we aren't always sitting at our desk it is best to use the form because it is guaranteed to be seen by all who are present at the time.

'''Office Hours''': GACRC staff are located in the Computing Services Building (formerly called Statistics Building), rooms 101 to 108. Our office is open Monday through Friday from 9am until 5pm. You are welcome to stop by and ask questions, or you can schedule an appointment using the [https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC General Support].

'''Directions''': The Computing Services Building is located at 101 Cedar Street, Athens, GA 30602, on the corner of Cedar Street and East Campus Rd. As you enter the building from the entrance on Cedar Street, on the East Campus Rd. end of the building, there are stairs leading down to the first floor. Our offices are on your left, as you come down those stairs.

Getting Help

2018-11-14T16:43:59Z

Yhuang:

At Nov 14, 2018, we change our ticketing system to the EITS GACRC TeamDynamic ticking system. To facilitate the process of help, the new system has specific entries for different subjects of requests.

Here is the landing page of all entries for help:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC Support Entry]

For requests of troubleshooting:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 Troubleshooting]

For requests of software installation:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 Software Installation]

For request of general help:

[https://uga.teamdynamix.com/TDClient/Requests/ServiceCatalog?CategoryID=11593 GACRC General Support]

This ticking system needs MYID to log in.

The primary way to contact us for help and initial consultation is via our support form. You can also call the EITS Help Desk at 542-3106 and they will either redirect your call to one of us, or enter a support ticket on your behalf. You are welcome to email or call us directly, but because we aren't always sitting at our desk it is best to use the form because it is guaranteed to be seen by all who are present at the time.

'''Office Hours''': GACRC staff are located in the Computing Services Building (formerly called Statistics Building), rooms 101 to 108. Our office is open Monday through Friday from 9am until 5pm. You are welcome to stop by and ask questions, or you can schedule an appointment using the [http://help.gacrc.uga.edu/ GACRC Support Form].

'''Directions''': The Computing Services Building is located at 101 Cedar Street, Athens, GA 30602, on the corner of Cedar Street and East Campus Rd. As you enter the building from the entrance on Cedar Street, on the East Campus Rd. end of the building, there are stairs leading down to the first floor. Our offices are on your left, as you come down those stairs.

Installing Applications

2018-09-25T18:29:45Z

Yhuang:

[[Category:Sapelo2]]

[[Build Applications on Sapelo2]]

Installing Applications

2018-08-23T18:19:16Z

Yhuang:

[[Category:Sapelo]][[Category:Sapelo2]]

[[Build Applications on Sapelo2]]

StringTie-Teaching

2018-08-15T19:47:14Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
1.3.4d

=== Author / Distributor ===

[http://ccb.jhu.edu/software/stringtie/ StringTie]

=== Description ===
"StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts."
More details are at [http://ccb.jhu.edu/software/stringtie/ StringTie]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/StringTie/1.3.4d-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml StringTie/1.3.4d-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_StringTie 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=StringTie.%j.out 
<nowiki>#</nowiki>SBATCH --error=StringTie.%j.err 

cd $SLURM_SUBMIT_DIR 
ml StringTie/1.3.4d-foss-2016b 
stringtie [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml StringTie/1.3.4d-foss-2016b
stringtie --help
StringTie v1.3.4d usage:
stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]
[-C <coverage_file_name>] [-c <min_bundle_cov>] [-g <bdist>] [-u]
[-e] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B | -b <dir_path>}
Assemble RNA-Seq alignments into potential transcripts.
Options:
--version : print just the version at stdout and exit
-G reference annotation to use for guiding the assembly process (GTF/GFF3)
--rf assume stranded library fr-firststrand
--fr assume stranded library fr-secondstrand
-l name prefix for output transcripts (default: STRG)
-f minimum isoform fraction (default: 0.1)
-m minimum assembled transcript length (default: 200)
-o output path/file name for the assembled transcripts GTF (default: stdout)
-a minimum anchor length for junctions (default: 10)
-j minimum junction coverage (default: 1)
-t disable trimming of predicted transcripts based on coverage
(default: coverage trimming is enabled)
-c minimum reads per bp coverage to consider for transcript assembly
(default: 2.5)
-v verbose (log bundle processing details)
-g gap between read mappings triggering a new bundle (default: 50)
-C output a file with reference transcripts that are covered by reads
-M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
-p number of threads (CPUs) to use (default: 1)
-A gene abundance estimation output file
-B enable output of Ballgown table files which will be created in the
same directory as the output GTF (requires -G, -o recommended)
-b enable output of Ballgown table files but these files will be
created under the directory path given as <dir_path>
-e only estimate the abundance of given reference transcripts (requires -G)
-x do not assemble any transcripts on the given reference sequence(s)
-u no multi-mapping correction (default: correction enabled)
-h print this usage message and exit

Transcript merge usage mode:
stringtie --merge [Options] { gtf_list | strg1.gtf ...}
With this option StringTie will assemble transcripts from multiple
input files generating a unified non-redundant set of isoforms. In this mode
the following options are available:
-G <guide_gff> reference annotation to include in the merging (GTF/GFF3)
-o <out_gtf> output file name for the merged transcripts GTF
(default: stdout)
-m <min_len> minimum input transcript length to include in the merge
(default: 50)
-c <min_cov> minimum input transcript coverage to include in the merge
(default: 0)
-F <min_fpkm> minimum input transcript FPKM to include in the merge
(default: 1.0)
-T <min_tpm> minimum input transcript TPM to include in the merge
(default: 1.0)
-f <min_iso> minimum isoform fraction (default: 0.01)
-g <gap_len> gap between transcripts to merge together (default: 250)
-i keep merged transcripts with retained introns; by default
these are not kept unless there is strong evidence for them
-l <label> name prefix for output transcripts (default: MSTRG)

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://ccb.jhu.edu/software/stringtie/ StringTie]

=== System ===
64-bit Linux

StringTie-Teaching

2018-08-15T19:47:06Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
1.3.3

=== Author / Distributor ===

[http://ccb.jhu.edu/software/stringtie/ StringTie]

=== Description ===
"StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts."
More details are at [http://ccb.jhu.edu/software/stringtie/ StringTie]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/StringTie/1.3.3-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml StringTie/1.3.3-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_StringTie 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=StringTie.%j.out 
<nowiki>#</nowiki>SBATCH --error=StringTie.%j.err 

cd $SLURM_SUBMIT_DIR 
ml StringTie/1.3.3-foss-2016b 
stringtie [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml StringTie/1.3.3-foss-2016b
stringtie --help
StringTie v1.3.3 usage:
stringtie <input.bam ..> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
[-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-f <min_iso>]
[-C <coverage_file_name>] [-c <min_bundle_cov>] [-g <bdist>] [-u]
[-e] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B | -b <dir_path>}
Assemble RNA-Seq alignments into potential transcripts.
Options:
--version : print just the version at stdout and exit
-G reference annotation to use for guiding the assembly process (GTF/GFF3)
--rf assume stranded library fr-firststrand
--fr assume stranded library fr-secondstrand
-l name prefix for output transcripts (default: STRG)
-f minimum isoform fraction (default: 0.1)
-m minimum assembled transcript length (default: 200)
-o output path/file name for the assembled transcripts GTF (default: stdout)
-a minimum anchor length for junctions (default: 10)
-j minimum junction coverage (default: 1)
-t disable trimming of predicted transcripts based on coverage
(default: coverage trimming is enabled)
-c minimum reads per bp coverage to consider for transcript assembly
(default: 2.5)
-v verbose (log bundle processing details)
-g gap between read mappings triggering a new bundle (default: 50)
-C output a file with reference transcripts that are covered by reads
-M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
-p number of threads (CPUs) to use (default: 1)
-A gene abundance estimation output file
-B enable output of Ballgown table files which will be created in the
same directory as the output GTF (requires -G, -o recommended)
-b enable output of Ballgown table files but these files will be
created under the directory path given as <dir_path>
-e only estimate the abundance of given reference transcripts (requires -G)
-x do not assemble any transcripts on the given reference sequence(s)
-u no multi-mapping correction (default: correction enabled)
-h print this usage message and exit

Transcript merge usage mode:
stringtie --merge [Options] { gtf_list | strg1.gtf ...}
With this option StringTie will assemble transcripts from multiple
input files generating a unified non-redundant set of isoforms. In this mode
the following options are available:
-G <guide_gff> reference annotation to include in the merging (GTF/GFF3)
-o <out_gtf> output file name for the merged transcripts GTF
(default: stdout)
-m <min_len> minimum input transcript length to include in the merge
(default: 50)
-c <min_cov> minimum input transcript coverage to include in the merge
(default: 0)
-F <min_fpkm> minimum input transcript FPKM to include in the merge
(default: 1.0)
-T <min_tpm> minimum input transcript TPM to include in the merge
(default: 1.0)
-f <min_iso> minimum isoform fraction (default: 0.01)
-g <gap_len> gap between transcripts to merge together (default: 250)
-i keep merged transcripts with retained introns; by default
these are not kept unless there is strong evidence for them
-l <label> name prefix for output transcripts (default: MSTRG)

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://ccb.jhu.edu/software/stringtie/ StringTie]

=== System ===
64-bit Linux

Bowtie2-Teaching

2018-08-15T19:44:21Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.3.4.1

=== Author / Distributor ===

[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Description ===
"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.4.1-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml Bowtie2/2.3.4.1-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Bowtie2 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Bowtie2.%j.out 
<nowiki>#</nowiki>SBATCH --error=Bowtie2.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Bowtie2/2.3.4.1-foss-2016b 
bowtie2 [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Bowtie2/2.3.4.1-foss-2016b
bowtie2 -h
Bowtie 2 version 2.3.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved } [-S <sam>]

<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
 Files with interleaved paired-end FASTQ reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<sam> File for SAM output (default: stdout)

<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

Input:
-q query input files are FASTQ .fq/.fastq (default)
--tab5 query input files are TAB5 .tab5
--tab6 query input files are TAB6 .tab6
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-F k:<int>,i:<int> query input files are continuous FASTA where reads
are substrings (k-mers) extracted from a FASTA file <s>
and aligned at offsets 1, 1+i, 1+2i ... end of reference
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers

Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)

Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)

Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful

Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)

Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all

Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--no-head suppress header lines, i.e. lines starting with @
--no-sq suppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non-standard SAM.
--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share

Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== System ===
64-bit Linux

Bowtie2-Teaching

2018-08-15T19:44:14Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.3.3

=== Author / Distributor ===

[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Description ===
"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Bowtie2/2.3.3-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml Bowtie2/2.3.3-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Bowtie2 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Bowtie2.%j.out 
<nowiki>#</nowiki>SBATCH --error=Bowtie2.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Bowtie2/2.3.3-foss-2016b 
bowtie2 [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Bowtie2/2.3.3-foss-2016b
bowtie2 -h
Bowtie 2 version 2.3.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved } [-S <sam>]

<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
 Files with interleaved paired-end FASTQ reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<sam> File for SAM output (default: stdout)

<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

Input:
-q query input files are FASTQ .fq/.fastq (default)
--tab5 query input files are TAB5 .tab5
--tab6 query input files are TAB6 .tab6
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers

Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)

Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)

Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful

Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)

Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all

Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--no-head suppress header lines, i.e. lines starting with @
--no-sq suppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
--sam-noqname-trunc Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non-standard SAM.
--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN

Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share

Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== System ===
64-bit Linux

Bowtie2-Teaching

2018-08-15T19:44:07Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.2.3

=== Author / Distributor ===

[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Description ===
"Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."
More details are at [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Bowtie2/2.2.3-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml Bowtie2/2.2.3-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Bowtie2 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Bowtie2.%j.out 
<nowiki>#</nowiki>SBATCH --error=Bowtie2.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Bowtie2/2.2.3-foss-2016b 
bowtie2 [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Bowtie2/2.2.3-foss-2016b
bowtie2 -h
Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<sam> File for SAM output (default: stdout)

<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

Input:
-q query input files are FASTQ .fq/.fastq (default)
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers

Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)

Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)

Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful

Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)

Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--no-dovetail not concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all

Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-head supppress header lines, i.e. lines starting with @
--no-sq supppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.

Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share

Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]

=== System ===
64-bit Linux

Java-Teaching

2018-08-15T19:41:57Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===
1.8.0_144

=== Author / Distributor ===

[http://java.com/ Java]

=== Description ===
"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers."
More details are at [http://java.com/ Java]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Java/1.8.0_144

To use this version, please load the module with
<pre class="gscript">
ml Java/1.8.0_144
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Java 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Java.%j.out 
<nowiki>#</nowiki>SBATCH --error=Java.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Java/1.8.0_144 
java [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Java/1.8.0_144
java
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server,
because you are running on a server-class machine.

-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://java.com/ Java]

=== System ===
64-bit Linux

Java-Teaching

2018-08-15T19:41:50Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===
1.8.0_141

=== Author / Distributor ===

[http://java.com/ Java]

=== Description ===
"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers."
More details are at [http://java.com/ Java]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Java/1.8.0_141

To use this version, please load the module with
<pre class="gscript">
ml Java/1.8.0_141
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Java 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Java.%j.out 
<nowiki>#</nowiki>SBATCH --error=Java.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Java/1.8.0_141 
java [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Java/1.8.0_141
java
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server,
because you are running on a server-class machine.

-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://java.com/ Java]

=== System ===
64-bit Linux

Java-Teaching

2018-08-15T19:41:43Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===
1.8.0_121

=== Author / Distributor ===

[http://java.com/ Java]

=== Description ===
"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers."
More details are at [http://java.com/ Java]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Java/1.8.0_121

To use this version, please load the module with
<pre class="gscript">
ml Java/1.8.0_121
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Java 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Java.%j.out 
<nowiki>#</nowiki>SBATCH --error=Java.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Java/1.8.0_121 
java [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Java/1.8.0_121
java
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server,
because you are running on a server-class machine.

-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://java.com/ Java]

=== System ===
64-bit Linux

Java-Teaching

2018-08-15T19:41:35Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===
1.8.0_112

=== Author / Distributor ===

[http://java.com/ Java]

=== Description ===
"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers."
More details are at [http://java.com/ Java]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Java/1.8.0_112

To use this version, please load the module with
<pre class="gscript">
ml Java/1.8.0_112
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Java 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Java.%j.out 
<nowiki>#</nowiki>SBATCH --error=Java.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Java/1.8.0_112 
java [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Java/1.8.0_112
java
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server,
because you are running on a server-class machine.

-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://java.com/ Java]

=== System ===
64-bit Linux

Java-Teaching

2018-08-15T19:41:27Z

Yhuang:

[[Category:Teaching]][[Category:Software]][[Category:Programming]]
=== Category ===

Programming

=== Program On ===

Teaching

=== Version ===
1.8.0_92

=== Author / Distributor ===

[http://java.com/ Java]

=== Description ===
"Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers."
More details are at [http://java.com/ Java]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/Java/1.8.0_92

To use this version, please load the module with
<pre class="gscript">
ml Java/1.8.0_92
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_Java 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=Java.%j.out 
<nowiki>#</nowiki>SBATCH --error=Java.%j.err 

cd $SLURM_SUBMIT_DIR 
ml Java/1.8.0_92 
java [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Java/1.8.0_92
java
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
where options include:
-d32 use a 32-bit data model if available
-d64 use a 64-bit data model if available
-server to select the "server" VM
The default VM is server,
because you are running on a server-class machine.

-cp <class search path of directories and zip/jar files>
-classpath <class search path of directories and zip/jar files>
A : separated list of directories, JAR archives,
and ZIP archives to search for class files.
-D<name>=<value>
set a system property
-verbose:[class|gc|jni]
enable verbose output
-version print product version and exit
-version:<value>
Warning: this feature is deprecated and will be removed
in a future release.
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
Warning: this feature is deprecated and will be removed
in a future release.
include/exclude user private JREs in the version search
-? -help print this help message
-X print help on non-standard options
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions with specified granularity
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions with specified granularity
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-splash:<imagepath>
show splash screen with specified image
See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [http://java.com/ Java]

=== System ===
64-bit Linux

StringTie-Teaching

2018-08-15T19:29:04Z

Yhuang:

StringTie-Teaching

2018-08-15T19:28:57Z

Yhuang:

Bowtie2-Teaching

2018-08-15T19:26:25Z

Yhuang:

Bowtie2-Teaching

2018-08-15T19:26:16Z

Yhuang:

Bowtie2-Teaching

2018-08-15T19:26:08Z

Yhuang:

Java-Teaching

2018-08-15T19:23:47Z

Yhuang:

Java-Teaching

2018-08-15T19:23:39Z

Yhuang:

Java-Teaching

2018-08-15T19:23:31Z

Yhuang:

Java-Teaching

2018-08-15T19:23:22Z

Yhuang:

Java-Teaching

2018-08-15T19:23:15Z

Yhuang:

StringTie-Teaching

2018-08-15T16:26:22Z

Yhuang:

StringTie-Teaching

2018-08-15T16:26:18Z

Yhuang: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.3.3 === A..."

HISAT2-Teaching

2018-08-15T16:26:04Z

Yhuang: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.1.0 === A..."

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.1.0

=== Author / Distributor ===

[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

=== Description ===
"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome)."
More details are at [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

=== Running Program ===

The last version of this application is at /usr/local/apps/eb/HISAT2/2.1.0-foss-2016b

To use this version, please load the module with
<pre class="gscript">
ml HISAT2/2.1.0-foss-2016b
</pre>

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_HISAT2 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=HISAT2.%j.out 
<nowiki>#</nowiki>SBATCH --error=HISAT2.%j.err 

cd $SLURM_SUBMIT_DIR 
ml HISAT2/2.1.0-foss-2016b 
hisat2 [options] 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml HISAT2/2.1.0-foss-2016b
hisat2 -help
HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage:
hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <sam>]

<ht2-idx> Index filename prefix (minus trailing .X.ht2).
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<SRA accession number> Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654.
<sam> File for SAM output (default: stdout)

<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

Input:
-q query input files are FASTQ .fq/.fastq (default)
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers
--sra-acc SRA accession ID

Alignment:
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)

Spliced Alignment:
--pen-cansplice <int> penalty for a canonical splice site (0)
--pen-noncansplice <int> penalty for a non-canonical splice site (12)
--pen-canintronlen <func> penalty for long introns (G,-8,1) with canonical splice sites
--pen-noncanintronlen <func> penalty for long introns (G,-8,1) with noncanonical splice sites
--min-intronlen <int> minimum intron length (20)
--max-intronlen <int> maximum intron length (500000)
--known-splicesite-infile <path> provide a list of known splice sites
--novel-splicesite-outfile <path> report a list of splice sites
--novel-splicesite-infile <path> provide a list of novel splice sites
--no-temp-splicesite disable the use of splice sites found
--no-spliced-alignment disable spliced alignment
--rna-strandness <string> specify strand-specific information (unstranded)
--tmo reports only those alignments within known transcriptome
--dta reports alignments tailored for transcript assemblers
--dta-cufflinks reports alignments tailored specifically for cufflinks
--avoid-pseudogene tries to avoid aligning reads to pseudogenes (experimental option)�
--no-templatelen-adjustment disables template length adjustment for RNA-seq reads

Scoring:
--mp <int>,<int> max and min penalties for mismatch; lower qual = lower penalty <6,2>
--sp <int>,<int> max and min penalties for soft-clipping; lower qual = lower penalty <2,1>
--no-softclip no soft-clipping
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(L,0.0,-0.2)

Reporting:
-k <int> (default: 5) report up to <int> alns per read

Paired-end:
-I/--minins <int> minimum fragment length (0), only valid with --no-spliced-alignment
-X/--maxins <int> maximum fragment length (500), only valid with --no-spliced-alignment
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads

Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--summary-file print alignment summary to this file.
--new-summary print alignment summary in a new style, which is more machine-friendly.
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-head supppress header lines, i.e. lines starting with @
--no-sq supppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.

Performance:
-o/--offrate <int> override offrate of index; must be >= index's offrate
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'hisat2's can share

Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--remove-chrname remove 'chr' from reference names in alignment
--add-chrname add 'chr' to reference names in alignment
--version print version information and quit
-h/--help print this usage message

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]

=== System ===
64-bit Linux

Bowtie2-Teaching

2018-08-15T16:23:28Z

Yhuang:

Bowtie2-Teaching

2018-08-15T16:23:23Z

Yhuang: