Singularity - Revision history

Shtsai at 14:02, 10 January 2022

2022-01-10T14:02:01Z

← Older revision		Revision as of 10:02, 10 January 2022
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	=== Loading Singularity ===		=== Loading Singularity ===
	Singularity is installed on all compute nodes on Sapelo2~~. In~~ order to access ~~that executables~~ you ~~have to load~~ the ~~Singularity module.~~		Singularity is installed on all compute nodes on Sapelo2 and you don't need to load any modules in order to access it. For example, you can run the following from an interactive session or in a batch job:
	<pre>		<pre>
	~~$ module load Singularity~~
	$ singularity --help		$ singularity --help
	USAGE: singularity [global options...] <command> [command options...] ...		USAGE: singularity [global options...] <command> [command options...] ...
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	</pre>		</pre>

			More information on how to use Singularity on Sapelo2 is available on the [[Software on Sapelo2]] page.

	=== Using BioContainer containers ===		=== Using BioContainer containers ===

Raj76: /* Preparing the database */

2017-12-22T20:35:07Z

Preparing the database

@@ Line 149: / Line 149: @@
 </pre>
-====== Preparing the database ======
+====== Running blastp search ======
 Now that we have a database created we can do an alignment against it as follows.
 <pre>
@@ Line 167: / Line 167: @@
 You could have used the existing blast databases in /db to perform the alignment by specifying

Raj76: /* Using BioContainer containers */

2017-12-22T20:34:01Z

Using BioContainer containers

@@ Line 107: / Line 107: @@
 ===== Accessing the cluster filesystem from inside the container =====
 The Singularity application on Sapelo2 has been pre-configured to mount the /home/$USER, /db, /lscratch, and /lustre1 filesystems inside the container.
 ===== Running Blast =====
@@ Line 124: / Line 137: @@
 ====== Preparing the database ======
 We need to prepare the zebrafish database with '''makeblastdb''' for the search.

Raj76: /* Using BioContainer containers */

2017-12-22T20:20:20Z

Using BioContainer containers

@@ Line 104: / Line 104: @@
 You now have a blast.simg image that can be used to run blast using Singularity.
 ===== Running Blast =====
@@ Line 120: / Line 123: @@
 </pre>
 ====== Preparing the database ======
-We need to prepare the zebrafish database with '''makeblastdb''' for the search. Before we do that let's understand how to access the Sapelo2 file systems from inside the container.
+We need to prepare the zebrafish database with '''makeblastdb''' for the search.

Raj76: /* Using BioContainer containers */

2017-12-22T16:56:01Z

Using BioContainer containers

@@ Line 109: / Line 109: @@
 $ singularity exec blast.simg blastp -help
 </pre>
-This will print the help page for '''blastp''' tool. The command '''singularity exec blast.simg'''
+This will print the help page for '''blastp''' tool. The command '''singularity exec blast.simg''' tells singularity that it is going to execute the command that follows inside the blast.simg container.

Raj76: /* Using BioContainer containers */

2017-12-22T16:44:08Z

Using BioContainer containers

← Older revision		Revision as of 12:44, 22 December 2017
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	In order to use a pre built container, one has to "pull" the container from the container registry.		In order to use a pre built container, one has to "pull" the container from the container registry.
	The command to pull a blast container from BioContainer docker registry is as below:		The command to pull a blast container from BioContainer docker registry is as below:

	<pre>		<pre>
	$ mkdir /home/raj76/test		$ mkdir /home/raj76/test
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	$		$
	</pre>		</pre>

			You now have a blast.simg image that can be used to run blast using Singularity.

			===== Running Blast =====
			<pre>
			$ singularity exec blast.simg blastp -help
			</pre>
			This will print the help page for '''blastp''' tool. The command '''singularity exec blast.simg'''

Raj76: /* Pulling containers from BioContainers */

2017-12-22T16:38:51Z

Pulling containers from BioContainers

@@ Line 52: / Line 52: @@
 </pre>
-=== Pulling containers from BioContainers ===
+=== Using BioContainer containers ===
 [https://biocontainers.pro/ BioContainers] is an open source and community-driven framework which provides system-agnostic executable environments for bioinformatics software. BioContainers framework allows software to be installed and executed under an isolated and controllable environment.

Raj76 at 16:26, 22 December 2017

2017-12-22T16:26:00Z

← Older revision		Revision as of 12:26, 22 December 2017
Line 51:		Line 51:

	</pre>		</pre>

			=== Pulling containers from BioContainers ===
			[https://biocontainers.pro/ BioContainers] is an open source and community-driven framework which provides system-agnostic executable environments for bioinformatics software. BioContainers framework allows software to be installed and executed under an isolated and controllable environment.

Raj76: /* Using Singularity containers on Sapelo2 */

2017-12-22T16:23:27Z

Using Singularity containers on Sapelo2

← Older revision		Revision as of 12:23, 22 December 2017
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	The Sapelo2 cluster has the ability to run Singularity containers. [http://singularity.lbl.gov/ Singularity] containers are docker like containers that are HPC friendly.		The Sapelo2 cluster has the ability to run Singularity containers. [http://singularity.lbl.gov/ Singularity] containers are docker like containers that are HPC friendly.


			=== Loading Singularity ===
			Singularity is installed on all compute nodes on Sapelo2. In order to access that executables you have to load the Singularity module.
			<pre>
			$ module load Singularity
			$ singularity --help
			USAGE: singularity [global options...] <command> [command options...] ...

			GLOBAL OPTIONS:
			-d\|--debug Print debugging information
			-h\|--help Display usage summary
			-s\|--silent Only print errors
			-q\|--quiet Suppress all normal output
			--version Show application version
			-v\|--verbose Increase verbosity +1
			-x\|--sh-debug Print shell wrapper debugging information

			GENERAL COMMANDS:
			help Show additional help for a command or container
			selftest Run some self tests for singularity install

			CONTAINER USAGE COMMANDS:
			exec Execute a command within container
			run Launch a runscript within container
			shell Run a Bourne shell within container
			test Launch a testscript within container

			CONTAINER MANAGEMENT COMMANDS:
			apps List available apps within a container
			bootstrap Deprecated use build instead
			build Build a new Singularity container
			check Perform container lint checks
			inspect Display container's metadata
			mount Mount a Singularity container image
			pull Pull a Singularity/Docker container to $PWD

			COMMAND GROUPS:
			image Container image command group
			instance Persistent instance command group


			CONTAINER USAGE OPTIONS:
			see singularity help <command>

			For any additional help or support visit the Singularity
			website: http://singularity.lbl.gov/

			</pre>

Raj76: Created page with "== Using Singularity containers on Sapelo2 == The Sapelo2 cluster has the ability to run Singularity containers. [http://singularity.lbl.gov/ Singularity] containers are dock..."

2017-12-22T16:18:07Z

Created page with "== Using Singularity containers on Sapelo2 == The Sapelo2 cluster has the ability to run Singularity containers. [http://singularity.lbl.gov/ Singularity] containers are dock..."

New page

== Using Singularity containers on Sapelo2 ==

The Sapelo2 cluster has the ability to run Singularity containers. [http://singularity.lbl.gov/ Singularity] containers are docker like containers that are HPC friendly.