Globally installed software: Difference between revisions
| 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.
<source lang='bash'>
export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles
</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/ ----------------------------------------- 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