Globally installed software: Difference between revisions
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== Available as modules == | == Available as modules == | ||
* gcc | * acml | ||
* | * alphaimpute | ||
* python | * bamtools | ||
* R | * bcftools | ||
* beagle | |||
* blacs | |||
* blas | |||
* [[BLAST | BLAST+]] | |||
* bonnie++ | |||
* boost | |||
* [[bowtie2 | bowtie]] | |||
* [[canu | canu]] | |||
* cdo | |||
* cmgui | |||
* [[cuda | cuda]] | |||
* diamond | |||
* [[dmtcp | dmtcp]] | |||
* emos | |||
* fasttree | |||
* ferret | |||
* ffmpeg | |||
* fftw2 | |||
* fftw3 | |||
* flex | |||
* freebayes | |||
* gcc | |||
* gcta | |||
* gdal | |||
* gdb | |||
* geos | |||
* glibc | |||
* glimmer | |||
* glimmerHMM | |||
* globalarrays | |||
* grads | |||
* grib | |||
* gsl | |||
* [[hadoop | hadoop ]] | |||
* hdf4 | |||
* hdf5 | |||
* [[hmmer | hmmer]] | |||
* hpl | |||
* htslib | |||
* hwloc | |||
* ima2p | |||
* intel | |||
* intel-cluster-checker | |||
* intel-cluster-runtime | |||
* intel-tbb-oss | |||
* iozone | |||
* jasper | |||
* java | |||
* julia | |||
* lapack | |||
* [[matlab | 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 | RAxML]] | |||
* RRO | |||
* rstudio | |||
* [[samtools | samtools]] | |||
* scalapack | |||
* slurm | |||
* slurm-drmaa | |||
* snpEff | |||
* [[spark | SPARK]] | |||
* szip | |||
* torque | |||
* [[Trinity | trinity]] | |||
* udunits | |||
* vcftools | |||
* vim | |||
* zlib | |||
== Globally installed on all nodes == | == Globally installed on all nodes == | ||
| Line 16: | Line 110: | ||
== Available as global SHARED modules == | == Available as global SHARED modules == | ||
Software can be deposited in: | Software can be deposited in: | ||
/shared/apps/SHARED/ | |||
Modules can be found in: | Modules can be found in: | ||
/shared/modulefiles/SHARED/ | |||
{| width="90%" | {| width="90%" | ||
| Line 72: | Line 166: | ||
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. | 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. | ||
< | <pre> | ||
export MODULEPATH=$MODULEPATH: | export MODULEPATH=$MODULEPATH:/shared/apps/WUR/ABGC/modulefiles | ||
</ | </pre> | ||
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: | 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: | ||
< | <pre> | ||
source .bash_profile | source .bash_profile | ||
</ | </pre> | ||
This needs to be done only for terminals that are already open. Next time you login, <code>.bash_profile</code> will be loaded automatically. | 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. | You can check if the modules are found. | ||
< | <pre> | ||
module avail | module avail | ||
</ | </pre> | ||
This should give output that includes something similar to this: | This should give output that includes something similar to this: | ||
---------------------------------------- | ---------------------------------------- /shared/modulefiles/ ----------------------------------------- | ||
ALLPATHS-LG/48961 bwa/0.7.5a jellyfish/2.1.1 RepeatMasker/4.0.3 | 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 | augustus/2.7 cegma/2.4 MAFFT/7.130 RepeatModeler/1.0.7 | ||
| Line 97: | Line 191: | ||
== See also == | == See also == | ||
* [[ | * [[installation_by_users | Installing domain specific software: installation by users]] | ||
* [[Setting local variables]] | * [[Setting local variables]] | ||
* [[Installing_R_packages_locally | Installing R packages locally]] | * [[Installing_R_packages_locally | Installing R packages locally]] | ||
Latest revision as of 09:58, 16 June 2023
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:
/shared/apps/SHARED/
Modules can be found in:
/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.
export MODULEPATH=$MODULEPATH:/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:
---------------------------------------- /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