Globally installed software: Difference between revisions
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| Line 67: | Line 67: | ||
<source lang='bash'> | <source lang='bash'> | ||
export MODULEPATH=$MODULEPATH:/cm/shared/modulefiles | export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles | ||
</source> | </source> | ||
This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again: | This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again: | ||
| Line 81: | Line 81: | ||
This should give output that includes something similar to this: | This should give output that includes something similar to this: | ||
---------------------------------------- /cm/shared/modulefiles | ---------------------------------------- /cm/shared/modulefiles/ ----------------------------------------- | ||
ALLPATHS-LG/48961 bwa/0.7.5a jellyfish/2.1.1 RepeatMasker/4.0.3 | 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 | augustus/2.7 cegma/2.4 MAFFT/7.130 RepeatModeler/1.0.7 | ||
Revision as of 10:54, 3 September 2014
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 v0.2.5
Available as global SHARED modules
Software can be deposited in:
/cm/shared/apps/SHARED/
Modules can be found in:
/cm/shared/modulefiles/SHARED/
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.
export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles
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 .bash_profile
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.
module avail
This should give output that includes something similar to this:
---------------------------------------- /cm/shared/modulefiles/ ----------------------------------------- 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