Globally installed software

Available as modules

• gcc/4.8.1
• python/2.7.6
• python/3.3.3
• R/3.0.2

Globally installed on all nodes

• Perl5.10
• pigz
• Python2.6
• BioPerl v1.61
• bgzip
• tabix

Available as global SHARED modules

Modules can be found in:

 /cm/shared/modulefiles/SHARED/

• ALLPATHS-LG/48961
• augustus/2.7
• bedtools/2.18.0
• BLAST+/2.2.28
• blat/v35
• bowtie/2-2.2.1
• bowtie/1-1.0.0
• bwa/0.5.9
• bwa/0.7.5a
• cegma/2.4
• cufflinks/2.1.1
• exonerate/2.2.0-x86_64
• geneid/1.4.4
• genewise/2.2.3-rc7
• hmmer/3.1b1
• jellyfish/2.1.1
• MAFFT/7.130
• maker/2.28
• muscle/3.8.31
• Plink/1.07
• provean/1.1.3
• RepeatMasker/4.0.3
• RepeatModeler/1.0.7
• RAxML/8.0.0
• samtools/0.1.12a
• samtools/0.1.19
• snap/2013-11-29
• SOAPdenovo2/r240
• tophat/2.0.11
• Trinity/r20131110

Adding a custom module directory to your environment

To allow the module program to find the custom module directory, the location of that directory has to be added to MODULEPATH variable.

<source lang='bash'> export MODULEPATH=$MODULEPATH:/cm/shared/modulefiles/SHARED </source> This can be made permanent by adding this line of code to the .bash_profile file in the root of your home folder. To then load the modified MODULEPATH variable you have to load .bash_profile again: <source lang='bash'> source .bash_profile </source> This needs to be done only for terminals that are already open. Next time you login, .bash_profile will be loaded automatically.

You can check if the modules are found. <source lang='bash'> module avail </source> This should give output that includes something similar to this:

 ---------------------------------------- /cm/shared/modulefiles/SHARED/ -----------------------------------------
 ALLPATHS-LG/48961      bwa/0.7.5a             jellyfish/2.1.1        RepeatMasker/4.0.3
 augustus/2.7           cegma/2.4              MAFFT/7.130            RepeatModeler/1.0.7
 bedtools/2.18.0        cufflinks/2.1.1        maker/2.28             samtools/0.1.12a
 BLAST+/2.2.28          exonerate/2.2.0-x86_64 muscle/3.8.31          samtools/0.1.19
 blat/v35               geneid/1.4.4           plink/1.07             snap/2013-11-29
 bowtie/2-2.2.1         genewise/2.2.3-rc7     provean/1.1.3          SOAPdenovo2/r240
 bwa/0.5.9              hmmer/3.1b1            RAxML/8.0.0            tophat/2.0.11

See also

• Using the B4F Cluster
• Installing domain specific software: installation by users
• Setting local variables
• Installing R packages locally
• Setting up and using a virtual environment for Python3
• modules specific for ABGC