Globally installed software: Difference between revisions
| Line 28: | Line 28: | ||
* [[bwa_7.5 | bwa/0.7.5a]] | * [[bwa_7.5 | bwa/0.7.5a]] | ||
* [[cegma_2.4 | cegma/2.4]] | * [[cegma_2.4 | cegma/2.4]] | ||
* [[Cufflinks | cufflinks/2.1.1]] | |||
* [[exonerate_2.2.0 | exonerate/2.2.0-x86_64]] | * [[exonerate_2.2.0 | exonerate/2.2.0-x86_64]] | ||
* [[geneid_1.4.4 | geneid/1.4.4]] | * [[geneid_1.4.4 | geneid/1.4.4]] | ||
| Line 33: | Line 34: | ||
* [[hmmer_3.1 | hmmer/3.1b1]] | * [[hmmer_3.1 | hmmer/3.1b1]] | ||
* [[jellyfish_2.1.1 | jellyfish/2.1.1]] | * [[jellyfish_2.1.1 | jellyfish/2.1.1]] | ||
* [[maker_2.2.8 | maker/2.28]] | * [[MAFFT_7.130 | MAFFT/7.130]] | ||
* [[maker_2.2.8 | maker/2.28]] | |||
* [[Muscle_3.8.31 | muscle/3.8.31]] | |||
* [[Plink_1.07 | Plink/1.07]] | * [[Plink_1.07 | Plink/1.07]] | ||
* [[Provean_1.1.3 | provean/1.1.3]] | * [[Provean_1.1.3 | provean/1.1.3]] | ||
* [[RepeatMasker_4.0.3 | RepeatMasker/4.0.3]] | * [[RepeatMasker_4.0.3 | RepeatMasker/4.0.3]] | ||
* [[RepeatModeler_1.0.7 | RepeatModeler/1.0.7]] | * [[RepeatModeler_1.0.7 | RepeatModeler/1.0.7]] | ||
* [[RAxML8.0.0 | RAxML/8.0.0]] | |||
* [[samtools v0.1.12a | samtools/0.1.12a]] | * [[samtools v0.1.12a | samtools/0.1.12a]] | ||
* [[samtools v0.1.19 | samtools/0.1.19]] | * [[samtools v0.1.19 | samtools/0.1.19]] | ||
* [[snap | snap/2013-11-29]] | * [[snap | snap/2013-11-29]] | ||
* [[soapdenovo2_r240 | SOAPdenovo2/r240]] | * [[soapdenovo2_r240 | SOAPdenovo2/r240]] | ||
* [[tophat_2.0.11 | TopHat/2.0.11]] | |||
== Adding a custom module directory to your environment == | == Adding a custom module directory to your environment == | ||
Revision as of 17:38, 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
- 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
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/apps/WUR/ABGC/modulefiles ----------------------------------- bwa/0.5.9 bwa/0.7.5a
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