CBCB Software Modules
Starting in the Spring of 2015, communal CBCB Bioinformatics Software has been installed using GNU Modules.
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:
bash$ module avail 2>&1 | less
or
tcsh> module avail |& less
To add a module to your environment, use module add:
$ 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 /cbcb/sw. 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>
/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
- Use the
srcdirectory for storing and compiling source code. - Use the
localdirectory as the installation prefix. - Use the
modulesdirectory to store your modulefiles.
See #Installing Software below.
To make use of your personal module file directory, add the following to your ~/.bashrc:
module use /cbcb/sw/RedHat-7-x86_64/users/<username>/modules
Installing Software
Use the install_package.sh script to automatically compile software that uses ./configure; make; make install. 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
modulesdirectory!
For full details, read the README placed in your personal directory (/cbcb/sw/RedHat-7-x86_64/users/<username>). It's also available in the cbcb-sw Gitlab repository.
Listing All Modules
The command module avail only lists modulefiles that appear in directories that have been added to your $MODULEPATH environment variable (either by hand or via module use command).
To see all modulefiles that are available for your use in both the Common Modules and the User Modules:
cat /cbcb/sw/RedHat-7-x86_64/common/all_modules.txt
or see 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:
$ source /usr/share/Modules/init/${SHELL}
bash$ source /etc/profile.d/ummodules.sh
For more information, see the UMIACS wiki.
GNU Modules Cheatsheet
Ask for help:
module --help
List available modules:
$ 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:
$ module add blast
Add a specific version to your environment:
$ module add blast/2.2.31
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)
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