Globally installed software

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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
  • 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

Available as global SHARED modules

Software can be deposited in:

 /cm/shared/apps/SHARED/

Modules can be found in:

 /cm/shared/modulefiles/SHARED/

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

External links