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/
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