Globally installed software: Difference between revisions

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== Available as modules ==
== Available as modules ==
 
* acml
* gcc/4.8.1
* alphaimpute
* python/2.7.6
* bamtools
* python/3.3.3
* bcftools
* R/3.0.2
* 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 12: Line 105:
* Python2.6
* Python2.6
* BioPerl v1.61
* BioPerl v1.61
*
* [http://samtools.sourceforge.net/tabix.shtml bgzip]
* [http://samtools.sourceforge.net/tabix.shtml tabix v0.2.5]


== Available as global SHARED modules ==
== Available as global SHARED modules ==
Software can be deposited in:
  /shared/apps/SHARED/


Modules can be found in:
Modules can be found in:
   /cm/shared/modulefiles/SHARED/
   /shared/modulefiles/SHARED/


{| width="90%"
|- valign="top"
| width="30%" |
* [[allpathslg_48961 | ALLPATHS-LG/48961]]
* [[allpathslg 51910 | ALLPATHS-LG/51910]]
* [[ANGSD_0.614 | angsd/0.614]]
* [[augustus_2.7 | augustus/2.7]]
* [[augustus_2.7 | augustus/2.7]]
* [[bedtools2.18 | bedtools/2.18.0]]
* [[bedtools2.18 | bedtools/2.18.0]]
* [[BLAST | BLAST+/2.2.28]]   
* [[BLAST | BLAST+/2.2.28]]   
* [[blat_v35 |blat/v35]]
* [[blat_v35 |blat/v35]]
* [[bowtie2_v2.2.1 | bowtie/2-2.2.1]]
* [[bowtie1_v1.0.0 | bowtie/1-1.0.0]]
* [[bwa_5.9 | bwa/0.5.9]]   
* [[bwa_5.9 | bwa/0.5.9]]   
* [[bwa_7.5 | bwa/0.7.5a]]
* [[bwa_7.5 | bwa/0.7.5a]]
* [[cegma_2.4 | cegma/2.4]]   
* [[cegma_2.4 | cegma/2.4]]   
* [[Cufflinks | cufflinks/2.1.1]]
| width="30%" |
* [[exonerate_2.2.0 | exonerate/2.2.0-x86_64]]  
* [[exonerate_2.2.0 | exonerate/2.2.0-x86_64]]  
* [[geneid_1.4.4 | geneid/1.4.4]]
* [[geneid_1.4.4 | geneid/1.4.4]]
* [[genewise_2.2.3 | genewise/2.2.3-rc7]]     
* [[genewise_2.2.3 | genewise/2.2.3-rc7]]     
* [[gmap_2014-01-21 | gmap/2014-01-21]]
* [[hmmer_3.1 | hmmer/3.1b1]]
* [[hmmer_3.1 | hmmer/3.1b1]]
* [[maker_2.2.8 | maker/2.28]]     
* [[jellyfish_2.1.1 | jellyfish/2.1.1]]
* [[MAFFT_7.130 | MAFFT/7.130]]
* [[maker_2.2.8 | maker/2.28]]
* [[Muscle_3.8.31 | muscle/3.8.31]]     
* [[Plink_1.07 | Plink/1.07]]
* [[Plink_1.07 | Plink/1.07]]
* [[Provean_1.1.3 | provean/1.1.3]]    
* [[Plink_1.9 | Plink/1.9]]
* [[Provean_1.1.3 | provean/1.1.3]]
* [[RepeatMasker_4.0.3 | RepeatMasker/4.0.3]]
* [[RepeatMasker_4.0.3 | RepeatMasker/4.0.3]]
| width="30%" |
* [[RepeatModeler_1.0.7 | RepeatModeler/1.0.7]]
* [[RepeatModeler_1.0.7 | RepeatModeler/1.0.7]]
* [[RAxML8.0.0 | RAxML/8.0.0]]
* [[samtools v0.1.12a | samtools/0.1.12a]]
* [[samtools v0.1.12a | samtools/0.1.12a]]
* [[samtools v0.1.19 | samtools/0.1.19]]
* [[samtools v0.1.19 | samtools/0.1.19]]
* [[snap | snap/2013-11-29]]
* [[snap | snap/2013-11-29]]
* [[soapdenovo2_r240 | SOAPdenovo2/r240]]
* [[sra_toolkit_2.3.4 | sra-toolkit/2.3.4]]
* [[TopHat_2.0.11 | tophat/2.0.11]]
* [[Trinity_r20131110 | Trinity/r20131110]]
* [[wgs_assembler_8.1 | wgs-assembler/8.1]]
|}
== Adding a module to your current session ==
Use <code>module apropos</code> to find the module you wish to use, then <code>module load</code> to enable it.


== Adding a custom module directory to your environment ==
== Adding a custom module directory to your environment ==
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.  


<source lang='bash'>
<pre>
export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles
export MODULEPATH=$MODULEPATH:/shared/apps/WUR/ABGC/modulefiles
</source>
</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:
<source lang='bash'>
<pre>
source .bash_profile
source .bash_profile
</source>
</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.
<source lang='bash'>
<pre>
module avail
module avail
</source>
</pre>
This should give output that includes something similar to this:
This should give output that includes something similar to this:


   ----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
   ---------------------------------------- /shared/modulefiles/ -----------------------------------------
   bwa/0.5.9 bwa/0.7.5a
  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 ==
== See also ==
* [[Main_Page#Using_the_B4F_Cluster | Using the B4F Cluster]]
* [[installation_by_users | Installing domain specific software: installation by users]]
* [[Globally_installed_software | Globally installed software]]
* [[Domain_specific_software_on_B4Fcluster_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]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* [[ABGC_modules | modules specific for ABGC ]]


== External links ==
== External links ==

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

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

External links

Retrieved from "https://wiki.anunna.wur.nl/index.php?title=Globally_installed_software&oldid=2224"