Globally installed software: Difference between revisions
| Line 24: | Line 24: | ||
* [[blat_v35 |blat/v35]] | * [[blat_v35 |blat/v35]] | ||
* [[bowtie2_v2.2.1 | bowtie/2-2.2.1]] | * [[bowtie2_v2.2.1 | bowtie/2-2.2.1]] | ||
* [[bowtie1_v1.0.0 | bowtie/1-1.0.0]] | |||
* [[bwa_5.9 | bwa/0.5.9]] | * [[bwa_5.9 | bwa/0.5.9]] | ||
* [[bwa_7.5 | bwa/0.7.5a]] | * [[bwa_7.5 | bwa/0.7.5a]] | ||
| Line 46: | Line 47: | ||
* [[soapdenovo2_r240 | SOAPdenovo2/r240]] | * [[soapdenovo2_r240 | SOAPdenovo2/r240]] | ||
* [[TopHat_2.0.11 | tophat/2.0.11]] | * [[TopHat_2.0.11 | tophat/2.0.11]] | ||
* [[Trinity_r20131110 | Trinity/r20131110]] | |||
== Adding a custom module directory to your environment == | == Adding a custom module directory to your environment == | ||
Revision as of 22:55, 15 March 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
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