Modules

Overview

LinGA’s newest cluster, RubySky, utilizes the Modules package for environment configuration. By default “linga-default” and “linga-proxy” are loaded. To add the the most recent versions of applications into the environment use “linga-latest”. Specific modules can be loaded and unloaded as required.

Sections

Common Commands
Command Command Examples

Scripts and qsubs

Load Modules Automatically (.bashrc)

Current Modules

 


Common Commands

module list List currently loaded modules.
module avail List available packages.
module help [modulefile] Description of specified module.
module show [modulefile] Displays information about specified module, including environment changes, dependencies, software version and path.
module load [modulefile] Loads module or specifies which dependencies have not been loaded.
module unload [modulefile] Unloads specified module from environment.
module purge Unloads all loaded modules

More information can be found in the Module man page.
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Command Command Examples

module list

module list_blur

module avail

module avail_blurNote: This application list is out of date. See the current list here.

module help [modulefile]

module help_blur

module display [modulefile]

module display_blur
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Scripts and qsubs

When including modules in scripts and qsubs, it is best practice to specify modules and applications by version number. Over time, linga-latest and module handles will be updated with the newest applications; specifying versions of applications required allows for repeatability of jobs in the future.

Example:

module load tophat/tophat-2.0.4_gnu446

rather than

module load tophat

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Load Modules Automatically (.bashrc)

Modules can be automatically loaded on login by adding the module load command to a user’s .bashrc file. The .bashrc file is located in the top level of a user’s home directory. The following example shows a .bashrc file that automatically loads specific versions of samtools and tophat.


# .bashrc 
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

# User specific aliases and functions
module load samtools/samtools-0.1.18_gnu446
module load tophat/tophat-2.0.4_gnu446

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Current Modules*

linga-default
linga-latest
linga-proxy
CASAVA/CASAVA_v1.8.2_gnu446
CPAT/CPAT-1.2.1_Python-2.7.3_gnu446
EPACTS/EPACTS-3.2.3_gnu446_x86_64
GATK/GATK_2.2-16-g9f648cb_jar_x86_64
HTSeq/HTSeq-0.5.4p1_Python-2.7.3_gnu446
R/R-2.15.1_gnu-4.4.6
R/R-2.15.3_gnu-4.4.6
RSeQC/RSeQC-2.3.2_Python-2.7.3_gnu446
RSeQC/RSeQC-2.3.3_Python-2.7.3_gnu446
UCSCUtils/UCSCUtils-20130327_bin
bamtools/bamtools-20130116_gnu446_x86_64
bedtools/bedtools-2.17.0_gnu446_x86_64
boost/boost_1_51_0_gnu446
bowtie2/bowtie2-2.0.0-beta7_gnu446
cufflinks/cufflinks-2.0.2_gnu446
mach/mach-1.0.18.c_gnu446
merlin/merlin-1.1.2_gnu446
merlin/merlin-1.1.2_open452
minimac/minimac-beta-2012.8.15_bin
openmpi-x86_64
pedstats/pedstats-0.6.12_gnu446
picard/picard-1.81_jar_x86_64
plink/plink-1.07_gnu446
protobuf/protobuf-2.4.1_gnu446_x86_64
python/Python-2.7.3_gnu446
samtools/samtools-0.1.18_gnu446
shapeit/shapeit.v2.r644.linux.x86_64
tabix/tabix-0.2.6_gnu446_x86_64
tophat/tophat-2.0.4_gnu446
tophat/tophat-2.0.6_gnu446
vcftools/vcftools_0.1.10_gnu446_x86_64

*This list may be out of date. SSH into rubysky and type “module avail” for the current list.