CBCB Software Modules - Revision history

Mbaney at 18:43, 15 October 2021

2021-10-15T18:43:29Z

← Older revision		Revision as of 18:43, 15 October 2021
Line 154:		Line 154:
	* [mailto:abelew@umiacs.umd.edu Trey Belew]		* [mailto:abelew@umiacs.umd.edu Trey Belew]
	* [mailto:keith@umiacs.umd.edu Keith Hughitt]		* [mailto:keith@umiacs.umd.edu Keith Hughitt]
	* [mailto:welles@umiacs.umd.edu Welles Robinson]
	* [mailto:hiren@umiacs.umd.edu Hiren Karathia]
	* [mailto:schrist1@umd.edu Steve Christensen]		* [mailto:schrist1@umd.edu Steve Christensen]
	* [mailto:spatkar@umiacs.umd.edu Sushant Patkar]

Adric: /* Setup for non-interactive shells */ -- Remove Torque reference

2018-11-16T19:45:32Z

Setup for non-interactive shells: -- Remove Torque reference

← Older revision		Revision as of 19:45, 16 November 2018
Line 77:		Line 77:
	== Setup for non-interactive shells ==		== Setup for non-interactive shells ==

	Modules are already configured for interactive shells, but to use modules with non-interactive shells ~~such as [[Torque]]~~, add the following to your ~/.bashrc:		Modules are already configured for interactive shells, but to use modules with non-interactive shells, add the following to your ~/.bashrc:
	$ source /usr/share/Modules/init/${SHELL}		$ source /usr/share/Modules/init/${SHELL}
	bash$ source /etc/profile.d/ummodules.sh		bash$ source /etc/profile.d/ummodules.sh

Abelew at 19:03, 7 April 2017

2017-04-07T19:03:49Z

← Older revision		Revision as of 19:03, 7 April 2017
Line 1:		Line 1:
	Starting in the Spring of 2015, communal CBCB Bioinformatics Software has been installed using GNU Modules. ~~<span style="color: blue;">Please note that the instructions below are for use with Red Hat 7 machines only.</span>~~		Starting in the Spring of 2015, communal CBCB Bioinformatics Software has been installed using GNU Modules.

	== Common Modules ==		== Common Modules ==

Line 7:		Line 6:

	To see see what modules are available:		To see see what modules are available:
	$ module avail		bash$ module avail 2>&1 \| less
			or
			tcsh> module avail \|& less

	To add a module to your environment, use <code>module add</code>:		To add a module to your environment, use <code>module add</code>:
Line 77:		Line 78:

	Modules are already configured for interactive shells, but to use modules with non-interactive shells such as [[Torque]], add the following to your ~/.bashrc:		Modules are already configured for interactive shells, but to use modules with non-interactive shells such as [[Torque]], add the following to your ~/.bashrc:
	. /usr/share/Modules/init/~~bash~~		$ source /usr/share/Modules/init/${SHELL}
	. /etc/profile.d/ummodules.sh		bash$ source /etc/profile.d/ummodules.sh

	For more information, see the [https://wiki.umiacs.umd.edu/umiacs/index.php/Modules UMIACS wiki].		For more information, see the [https://wiki.umiacs.umd.edu/umiacs/index.php/Modules UMIACS wiki].
Line 88:		Line 89:

	List available modules:		List available modules:
	module avail		$ module avail

			Read the description of a module:
			$ module whatis blast

			Read the help text for a module:
			$ module help blast

	Add a module to your environment:		Add a module to your environment:
	module add blast		$ module add blast

			Add a specific version to your environment:
			$ module add blast/2.2.31

	List loaded modules:		List loaded modules:
	module list		$ module list

	Remove a module from your environment:		Remove a module from your environment:
	module rm blast		$ module rm blast

	Remove all modules from your environment:		Remove all modules from your environment:
	module purge		$ module purge

	Add a path to search for available modules:		Add a path to search for available modules:
	module use /cbcb/sw/RedHat-7-x86_64/users/lmendelo/modules		$ module use /cbcb/sw/RedHat-7-x86_64/users/lmendelo/modules

	See what changes a module makes to your environment:		See what changes a module makes to your environment:
	module show Python2/common/2.7.9		$ module show Python2/common/2.7.9

	== Maintainers ==		== Maintainers ==

Spatkar: /* Contact */

2017-03-06T20:12:14Z

Contact

← Older revision		Revision as of 20:12, 6 March 2017
Line 147:		Line 147:
	* [mailto:hiren@umiacs.umd.edu Hiren Karathia]		* [mailto:hiren@umiacs.umd.edu Hiren Karathia]
	* [mailto:schrist1@umd.edu Steve Christensen]		* [mailto:schrist1@umd.edu Steve Christensen]
			* [mailto:spatkar@umiacs.umd.edu Sushant Patkar]


	== See Also ==		== See Also ==

Schrist1 at 20:10, 6 March 2017

2017-03-06T20:10:37Z

← Older revision		Revision as of 20:10, 6 March 2017
Line 146:		Line 146:
	* [mailto:welles@umiacs.umd.edu Welles Robinson]		* [mailto:welles@umiacs.umd.edu Welles Robinson]
	* [mailto:hiren@umiacs.umd.edu Hiren Karathia]		* [mailto:hiren@umiacs.umd.edu Hiren Karathia]
			* [mailto:schrist1@umd.edu Steve Christensen]

	== See Also ==		== See Also ==

Hiren: /* Contact */

2017-03-06T20:09:21Z

Contact

← Older revision		Revision as of 20:09, 6 March 2017
Line 145:		Line 145:
	* [mailto:keith@umiacs.umd.edu Keith Hughitt]		* [mailto:keith@umiacs.umd.edu Keith Hughitt]
	* [mailto:welles@umiacs.umd.edu Welles Robinson]		* [mailto:welles@umiacs.umd.edu Welles Robinson]
			* [mailto:hiren@umiacs.umd.edu Hiren Karathia]

	== See Also ==		== See Also ==

Welles: /* Contact */

2017-03-06T20:08:41Z

Contact

← Older revision		Revision as of 20:08, 6 March 2017
Line 144:		Line 144:
	* [mailto:abelew@umiacs.umd.edu Trey Belew]		* [mailto:abelew@umiacs.umd.edu Trey Belew]
	* [mailto:keith@umiacs.umd.edu Keith Hughitt]		* [mailto:keith@umiacs.umd.edu Keith Hughitt]
	* [mailto:~~lmendelo~~@umiacs.umd.edu ~~Lee Mendelowitz~~]		* [mailto:welles@umiacs.umd.edu Welles Robinson]

	== See Also ==		== See Also ==

Keith: Add Trey's R module upgrade notes

2015-07-24T19:12:20Z

Add Trey's R module upgrade notes

@@ Line 107: / Line 107: @@
 See what changes a module makes to your environment:
   module show Python2/common/2.7.9
 == Contact ==

Lmendelo: /* Listing All Modules */

2015-06-19T15:39:22Z

Listing All Modules

← Older revision		Revision as of 15:39, 19 June 2015
Line 66:		Line 66:

	The command <code>module avail</code> only lists modulefiles that appear in directories that have been added to your <code>$MODULEPATH</code> environment variable (either by hand or via <code>module use</code> command).		The command <code>module avail</code> only lists modulefiles that appear in directories that have been added to your <code>$MODULEPATH</code> environment variable (either by hand or via <code>module use</code> command).
	To see all modulefiles that are available for your use in both ~~from~~ the Common Modules and ~~from~~ the User Modules:		To see all modulefiles that are available for your use in both the Common Modules and the User Modules:

	<pre>		<pre>

Lmendelo: /* User Modules */

2015-04-23T20:30:02Z

User Modules

← Older revision		Revision as of 20:30, 23 April 2015
Line 62:		Line 62:

	For full details, read the <code>README</code> placed in your personal directory (<code>/cbcb/sw/RedHat-7-x86_64/users/<username></code>). It's also available in the [https://gitlab.umiacs.umd.edu/cbcb/cbcb-sw/blob/master/templates/user_readme.md cbcb-sw Gitlab repository].		For full details, read the <code>README</code> placed in your personal directory (<code>/cbcb/sw/RedHat-7-x86_64/users/<username></code>). It's also available in the [https://gitlab.umiacs.umd.edu/cbcb/cbcb-sw/blob/master/templates/user_readme.md cbcb-sw Gitlab repository].

			=== Listing All Modules ===

			The command <code>module avail</code> only lists modulefiles that appear in directories that have been added to your <code>$MODULEPATH</code> environment variable (either by hand or via <code>module use</code> command).
			To see all modulefiles that are available for your use in both from the Common Modules and from the User Modules:

			<pre>
			cat /cbcb/sw/RedHat-7-x86_64/common/all_modules.txt
			</pre>

			or see [http://cbcb.umd.edu/~lmendelo/cbcb_modules/all_modules.txt here].

	== Setup for non-interactive shells ==		== Setup for non-interactive shells ==