Globally installed software

Available as modules

• acml
• alphaimpute
• bamtools
• bcftools
• beagle
• blacs
• blas
• BLAST+
• bonnie++
• boost
• bowtie
• canu
• cdo
• cmgui
• diamond
• dmtcp
• emos
• fasttree
• ferret
• ffmpeg
• fftw2
• fftw3
• flex
• freebayes
• gcc
• gcta
• gdal
• gdb
• geos
• glibc
• glimmer
• glimmerHMM
• globalarrays
• grads
• grib
• gsl
• hadoop
• hdf4
• hdf5
• hdf5_18
• hmmer
• hpl
• htslib
• hwloc
• ima2p
• intel
• intel-cluster-checker
• intel-cluster-runtime
• intel-tbb-oss
• iozone
• jasper
• java
• julia
• lapack
• matlab
• mixblup
• mpich
• mpiexec
• MRO
• muscle
• mvapich
• mvapich2
• ncbi-blast
• ncl
• nco
• ncview
• netcdf
• netcdf3-c++
• netperf
• octave
• open64
• openblas
• openlava
• openmpi
• oracle-instantclient
• pbspro
• phdf5
• picard
• plink
• prodigal
• python
• R
• ragel
• RAxML
• RRO
• rstudio
• samtools
• scalapack
• sge
• SHARED
• slurm
• slurm-drmaa
• snpEff
• spark
• szip
• torque
• trinity
• udunits
• vcftools
• vim
• zlib

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/

ALLPATHS-LG/48961 ALLPATHS-LG/51910 angsd/0.614 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 gmap/2014-01-21 hmmer/3.1b1 jellyfish/2.1.1 MAFFT/7.130 maker/2.28 muscle/3.8.31 Plink/1.07 Plink/1.9 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 sra-toolkit/2.3.4 tophat/2.0.11 Trinity/r20131110 wgs-assembler/8.1

Adding a module to your current session

Use module apropos to find the module you wish to use, then module load to enable it.

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