Globally installed software

Available as modules

• acml
• alphaimpute
• bamtools
• bcftools
• beagle
• blacs
• blas
• BLAST+
• bonnie++
• boost
• bowtie
• canu
• cdo
• cmgui
• cuda
• 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
• 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
• phdf5
• picard
• plink
• prodigal
• python
• R
• ragel
• RAxML
• RRO
• rstudio
• samtools
• scalapack
• 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.

export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles

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 .bash_profile

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.

module avail

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

• 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