Globally installed software: Difference between revisions
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* BioPerl v1.61 | * BioPerl v1.61 | ||
* | * | ||
== Available as global SHARED modules == | |||
Modules can be found in: | |||
/cm/shared/modulefiles/SHARED/ | |||
* [[augustus_2.7 | augustus/2.7]] | |||
* [[bedtools2.18 | bedtools/2.18.0]] | |||
* [[BLAST | BLAST+/2.2.28]] | |||
* [[blat_v35 |blat/v35]] | |||
* [[bwa_5.9 | bwa/0.5.9]] | |||
* [[bwa_7.5 | bwa/0.7.5a]] | |||
* [[cegma_2.4 | cegma/2.4]] | |||
* [[exonerate_2.2.0 | exonerate/2.2.0-x86_64]] | |||
* [[geneid_1.4.4 | geneid/1.4.4]] | |||
* [[genewise_2.2.3 | genewise/2.2.3-rc7]] | |||
* [[hmmer_3.1 | hmmer/3.1b1]] | |||
* [[maker_2.2.8 | maker/2.28]] | |||
* [[Plink_1.07 | Plink/1.07]] | |||
* [[Provean_1.1.3 | provean/1.1.3]] | |||
* [[RepeatMasker_4.0.3 | RepeatMasker/4.0.3]] | |||
* [[RepeatModeler_1.0.7 | RepeatModeler/1.0.7]] | |||
* [[samtools v0.1.12a | samtools/0.1.12a]] | |||
* [[samtools v0.1.19 | samtools/0.1.19]] | |||
* [[snap | snap/2013-11-29]] | |||
== Adding a custom module directory to your environment == | |||
To allow the <code>module</code> program to find the custom module directory, the location of that directory has to be added to <code>MODULEPATH</code> 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 <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: | |||
<source lang='bash'> | |||
source .bash_profile | |||
</source> | |||
This needs to be done only for terminals that are already open. Next time you login, <code>.bash_profile</code> 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 == | |||
* [[Main_Page#Using_the_B4F_Cluster | Using the B4F Cluster]] | |||
* [[Globally_installed_software | Globally installed software]] | |||
* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]] | |||
* [[Setting local variables]] | |||
* [[Installing_R_packages_locally | Installing R packages locally]] | |||
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]] | |||
== External links == | |||
Revision as of 09:48, 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/
- augustus/2.7
- bedtools/2.18.0
- BLAST+/2.2.28
- blat/v35
- bwa/0.5.9
- bwa/0.7.5a
- cegma/2.4
- exonerate/2.2.0-x86_64
- geneid/1.4.4
- genewise/2.2.3-rc7
- hmmer/3.1b1
- maker/2.28
- Plink/1.07
- provean/1.1.3
- RepeatMasker/4.0.3
- RepeatModeler/1.0.7
- samtools/0.1.12a
- samtools/0.1.19
- snap/2013-11-29
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
- Globally installed software
- Installing domain specific software: installation by users
- Setting local variables
- Installing R packages locally
- Setting up and using a virtual environment for Python3