IGV-Teaching: Difference between revisions
(Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.4.4 === Author / Di...") |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Category: | [[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] | ||
=== Category === | === Category === | ||
| Line 6: | Line 6: | ||
=== Program On === | === Program On === | ||
Teaching | |||
=== Version === | === Version === | ||
| Line 37: | Line 37: | ||
</pre> | </pre> | ||
Example running this on | Please note, IGV GUI can run from login node with | ||
Example running this on login node: | |||
<pre class="gcommand"> | <pre class="gcommand"> | ||
module load IGV/2.4.4-Java-1.8.0_144 | module load IGV/2.4.4-Java-1.8.0_144 | ||
sh /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144/igv.sh | sh /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144/igv.sh | ||
| Line 55: | Line 56: | ||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
=== Category === | |||
Bioinformatics | |||
=== Program On === | |||
=== Version === | |||
17.0.1 | |||
=== Author / Distributor === | |||
[http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act Artemis] | |||
=== Description === | |||
"Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation." | |||
More details are at [http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act Artemis] | |||
=== Running Program === | |||
The last version of this application is at /usr/local/apps/eb/Artemis/17.0.1-Java-1.8.0_144 | |||
To use this version, please load the module with | |||
<pre class="gscript"> | |||
ml Artemis/17.0.1-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<br> | |||
<nowiki>#</nowiki>SBATCH --job-name=j_Artemis<br> | |||
<nowiki>#</nowiki>SBATCH --partition=batch<br> | |||
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | |||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | |||
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> | |||
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br> | |||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | |||
<nowiki>#</nowiki>SBATCH --output=Artemis.%j.out<br> | |||
<nowiki>#</nowiki>SBATCH --error=Artemis.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | |||
ml Artemis/17.0.1-Java-1.8.0_144<br> | |||
act <u>[options]</u><br> | |||
</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> | |||
Revision as of 10:48, 7 February 2019
Category
Bioinformatics
Program On
Teaching
Version
2.4.4
Author / Distributor
To cite your use of IGV in your publication:
James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011), or
Helga Thorvaldsdottir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Briefings in Bioinformatics 2012.
Description
"The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations." more details at IGV
Running Program
Also refer to Running Jobs on Sapelo2
- Version 2.4.4, installed in /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144
To use this version of IGV, please first load the module with
module load IGV/2.4.4-Java-1.8.0_144
Please note, IGV GUI can run from login node with
Example running this on login node:
module load IGV/2.4.4-Java-1.8.0_144 sh /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144/igv.sh exit
Documentation
more details at IGV
Installation
source code from IGV
System
64-bit Linux
Category
Bioinformatics
Program On
Version
17.0.1
Author / Distributor
Description
"Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation." More details are at Artemis
Running Program
The last version of this application is at /usr/local/apps/eb/Artemis/17.0.1-Java-1.8.0_144
To use this version, please load the module with
ml Artemis/17.0.1-Java-1.8.0_144
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_Artemis
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Artemis.%j.out
#SBATCH --error=Artemis.%j.err
cd $SLURM_SUBMIT_DIR
ml Artemis/17.0.1-Java-1.8.0_144
act [options]
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, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh