View source for CBCB Software Modules

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>

== Common Modules ==

CBCB Software modules are already configured for interactive shells on Red Hat 7 machines - no additional setup is required. The module files are installed in the following location:
 /cbcb/sw/RedHat-7-x86_64/common/modules/release/latest

To see see what modules are available:
 $ module avail

To add a module to your environment, use <code>module add</code>:
 $ module add samtools/0.1.19

Note that you can also specify the software name without the version:
 $ module add samtools

Now samtools has been added to your environment:
 $ which samtools
 /cbcb/sw/RedHat-7-x86_64/common/local/samtools/0.1.19/bin/samtools

== User Modules ==

We have created some scripts to assist you with installing software and modules to your user directory in <code>/cbcb/sw</code>. We recommend that you use these scripts because this will help us share installed software among other CBCB users.

Run this initialization script to set up your directory structure:
 $ /cbcb/sw/RedHat-7-x86_64/common/scripts/init_cbcb_sw_user.sh

This will create a directory for you:
 $ tree /cbcb/sw/RedHat-7-x86_64/users/<username>

<pre>
/cbcb/sw/RedHat-7-x86_64/users/<username>
├── local
├── modules
│   └── <username>
│       └── env
├── module_template
├── README
├── scripts
│   ├── copy_module_template.sh
│   ├── init_install_vars.sh
│   └── install_package.sh
└── src
</pre>

* Use the <code>src</code> directory for storing and compiling source code.
* Use the <code>local</code> directory as the installation prefix.
* Use the <code>modules</code> directory to store your modulefiles.

See [[#Installing Software]] below.

To make use of your personal module file directory, add the following to your <code>~/.bashrc</code>:
 module use /cbcb/sw/RedHat-7-x86_64/users/<username>/modules


=== Installing Software ===

Use the <code>install_package.sh</code> script to automatically compile software that uses <code>./configure; make; make install</code>. The advantage to using this install script is that it will:
* use the standardized directory structure for personal software installation, and
* '''''automatically''''' create a module file for the software in your <code>modules</code> directory!


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 the Common Modules and 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 ==

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
 . /etc/profile.d/ummodules.sh

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

== GNU Modules Cheatsheet ==

Ask for help:
 module --help

List available modules:
 module avail

Add a module to your environment:
 module add blast

List loaded modules:
 module list

Remove a module from your environment:
 module rm blast

Remove all modules from your environment:
 module purge

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

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

== Maintainers ==

=== Creating a new release ===

=== Upgrading R ===

There are a couple scripts to hopefully make upgrading R easier.
Let us say that you are installing a new version of R and R libraries.
If that is (for example) version 3.2.1, then a set of commands might include:

 > cd $MOD/R/common
 > cp 3.2.0 3.2.1

Now edit 3.2.1 to include the new version and change anything of interest.

 > mkdir $STOW/Rext/3.2.1
 > module add R/common/3.2.1

Assuming that you edited the $MOD 3.2.1 file to tell it to load R version 3.2.1, then
$(which R) will show the new version and the module command will set the R_LIBS
variable to a new, empty directory.
 
 > cd $STOW/R/common
 > ./update_R.sh 3.2.0_list

This little shell script should call Bioconductor's biocLite() once for each
R library which was installed in 3.2.0.

(Adapted from /cbcb/sw/RedHat-7-x86_64/common/local/Rext/README.md)

== Contact ==

Brought to you by:

* [mailto:abelew@umiacs.umd.edu Trey Belew]
* [mailto:keith@umiacs.umd.edu Keith Hughitt]
* [mailto:welles@umiacs.umd.edu Welles Robinson]
* [mailto:hiren@umiacs.umd.edu Hiren  Karathia]

== See Also ==
* [https://wiki.umiacs.umd.edu/umiacs/index.php/Modules UMIACS wiki]
* [https://gitlab.umiacs.umd.edu/cbcb/cbcb-sw Repository on GitLab]
* [https://docs.google.com/presentation/d/1UgKtnjcqHlpLZU79hGXfkgvNtse-ksMQ_gJMFCVLKRw/edit?usp=sharing CBCB Software slides on Google Drive]