Software installed on Computerome
At Computerome we maintain an extensive and ever growing list of software available to our users.
This page describes how to use the software packages installed on the Computerome cluster.
To use this software you must first log in to the system, see SSH login to Computerome 2.0.
Using modules
Software installed on Computerome is managed using modules as described in the Environment Modules Project. Modules provide a mechanism to set/unset all environment variables related to a given package in one UNIX shell command. Modules are activated by default for users on Computerome. Computerome utilities for modules To help in finding tools, we have created a module 'computerome_utils' with a handful of small utilities - currently (2020.09.30): moduleavail <string> - list available environment modules Just load it and try it out $ module load tools computerome_utils/2.0 To list your currently available modules, type: The command will per default list something similar to this: Regular users should focus on modules located under where <module name> can be tools, ngs, shared, use.own etc. You can limit the number of listed modules, by adding the first letter(s) of the modulename to the To get basic information on the modulefiles, you can use To search for a particular string in the basic information on the modulefiles, you can use Example using Further information is available with Sometimes, the software you are looking for will not have its own module, but comes as part of a module. The most common examples of this are Anaconda (python) packages, Perl-modules, and R packages. In these cases, To add one or more modules, use Modules listed without version information (like Modules listed with version information (like Modules will report any If you get such a message, you can use Verify which modules are loaded To switch loaded modulefile1 with modulefile2, use To remove one or more modules, use module purge In case all modules need to be unloaded at once use: It is possible to permanently add, manipulate and remove modules in your login environment, by using the Add modulefile(s) to the shell’s initialization file in the user’s home directory. initprepend modulefile [modulefile...] Does the same as initadd but prepends the given modules to the beginning of the list. initrm modulefile... Remove modulefile(s) from the shell’s initialization files. initswitch modulefile1 modulefile2 Switch modulefile1 with modulefile2 in the shell’s initialization files. initlist List all of the modulefiles loaded from the shell’s initialization file. initclear Clear all of the modulefiles from the shell’s initialization files. Further information is available in MAN page for 'module'
Modules definitions are contained in so-called modulefiles located in several directories. The directory structure is dependent on the system.Listing and finding modules
moduleapropos [-i] <string> - search for string in module information
modulewhatis <string> - list module information
findintools [-i] <string> - search for string across all applications (modules, perl, anaconda, R)
findinanaconda [-i] <string> - search for string in Anaconda packages
findinperl [-i] <string> - search for string in Perl packages
findinr [-i] <string> - search for string in R packagesmodule avail
$ module avail
$ module avail
----------------------------------------------------------------------------------- /cm/local/modulefiles -----------------------------------------------------------------------------------
cluster-tools/8.2 cmd cmsub freeipmi/1.6.2 ipmitool/1.8.18 module-git ngs openldap python36 tools
cm-cloud-copy/8.2 cmsh dot gcc/8.2.0 lua/5.3.5 module-info null python2 shared
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/shared/modulefiles ----------------------------------------------------------------------
blacs/openmpi/gcc/64/1.1patch03 cuda10.1/blas/10.1.243 default-environment hwloc/1.11.11 openblas/dynamic(default)
blas/gcc/64/3.8.0 cuda10.1/fft/10.1.168 fftw2/openmpi/gcc/64/double/2.1.5 intel-tbb-oss/ia32/2019_20190410oss openblas/dynamic/0.2.20
bonnie++/1.97.3 cuda10.1/fft/10.1.243 fftw2/openmpi/gcc/64/float/2.1.5 intel-tbb-oss/intel64/2019_20190410oss openmpi/gcc/64/1.10.7
cm-pmix3/3.1.4 cuda10.1/nsight/10.1.168 fftw3/openmpi/gcc/64/3.3.8 iozone/3_482 openmpi/gcc/64/4.0.2
cuda/toolkit/10.1/10.1.168 cuda10.1/nsight/10.1.243 gdb/8.2 lapack/gcc/64/3.8.0 scalapack/openmpi/gcc/64/2.0.2
cuda/toolkit/10.1/10.1.243 cuda10.1/profiler/10.1.168 globalarrays/openmpi/gcc/64/5.7 mpich/ge/gcc/64/3.3 sge/2011.11p1
cuda/toolkit/101/10.1.168 cuda10.1/profiler/10.1.243 hdf5/1.10.1 mvapich2/gcc/64/2.3 slurm/18.08.8
cuda/toolkit/101/10.1.243 cuda10.1/toolkit/10.1.168 hdf5_18/1.8.20 netcdf/gcc/64/4.6.1
cuda10.1/blas/10.1.168 cuda10.1/toolkit/10.1.243 hpl/2.2 netperf/2.7.0
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/tools/modulefiles -----------------------------------------------------------------------
454/2.9 depot_tools/20160809 intel/perflibs/2018_update2 netphorest_human/2.1 samblaster/0.1.24
abawaca/20170520 diamond/0.7.9 intel/perflibs/2018_update3 netsurfp/1.0b samclip/0.2
abctoolbox/20090930 diamond/0.8.31 intel/perflibs/2018_update4 netsurfp/1.0d samstat/1.5.1
abra2/2.20 diamond/0.9.13 intel/perflibs/2019 nettle/3.5.1 samtools/0.1.18
abricate/0.5 diamond/0.9.24 intel/perflibs/2019_update2 netturnp/1.0a samtools/0.1.19
abricate/0.8.7 diginorm/20131102 intel/perflibs/2019_update3 new_fugue/20100602 samtools/1.2
abyss/2.0.2 disco/1.0 intel/perflibs/2019_update5 newick-utils/1.6 samtools/1.3.1
abyss/2.1.5 discovar/52188 intel/redist/2017.2.174 nextflow/0.31.1 samtools/1.4
activetcl/8.6.8.0 discovar/52488 intel/redist/2017_update4 nextflow/19.03.0-edge samtools/1.4.1
AdapterRemoval/2.1.3 discovardenovo/52488 intel/redist/2018 nextflow/19.07.0 samtools/1.5
adapterremoval/2.1.3 discovarexp/52242 intel/redist/2018_update1 nextflow/19.09.0-edge samtools/1.6
AdapterRemoval/2.1.7 dissect/1.2 intel/redist/2018_update3 ngb/2.5.1.374.1 samtools/1.7
adapterremoval/2.1.7 dlcpar/1.0 intel/redist/2018_update5 ngless/0.7.1 samtools/1.8
AdapterRemoval/2.2.0 docker-compose/1.21.2 intel/redist/2019 ngless/0.8.1 samtools/1.9
adapterremoval/2.2.0 dos2unix/7.3.1 intel/redist/2019_update2 ngless/0.9.1 sas/DEPRECATED/9.4
AdapterRemoval/2.2.1a dos2unix/7.4.0 interop/1.1.8 ngmlr/0.2.7 satsuma/3.0
adapterremoval/2.2.1a drop-seq_tools/2.0.0 interproscan/5.11-51.0 ngsadmix/32 savvy/1.2.0
AdapterRemoval/2.2.2 dropest/0.8.5 interproscan/5.13-52.0 ngsqctoolkit/2.3.3 sbcl/1.3.17
adapterremoval/2.2.2 dropest/20190401 interproscan/5.17-56.0 ngstools/20180814 scaffold/4.9.0
AdapterRemoval/2.2.4 dssp/2.0.4 interproscan/5.19-58.0 ngstools/20190624 scalpel/0.5.2
adapterremoval/2.2.4 dssp/2.2.1 interproscan/5.22-61.0 nim/0.16.0 schmutzi/1.5.5.5
admixture/1.3.0 duphold/0.1.5 interproscan/5.25-64.0 nim/1.0.0 schmutzi/20161010
admixture/1.23 ea-utils/1.1.2-806 interproscan/5.32-71.0 ninja/1.8.2 scipion-dev/1.1F
adolc/2.5.2 eager-gui/1.92.37 interproscan/5.36-75.0 ninja/1.9.0 scipion/1.0
adxv/1.9.10 eagle/2.3.5 ioapi/3.1 nlopt/2.4.2 scipion/1.0.0
adxv/1.9.11 eclipse-cpp/2018-09 iozone/3.434 nnlinplayer/1.0 scipion/1.0.1
adxv/1.9.12 eclipse-parallel/2018-09 iperf/2.0.5 nodejs/8.9.1_LTS scipion/1.1
agouti/0.3.3.1-gc8bd255 edirect/7.50 iperf/3.0.11 nodejs/9.2.0 scipion/1.2
albula/3.2.0-2 effectorp/1.0 iperf/3.1 nodejs/10.1.0 scipion/2.0.0
ale/20130717 effectorp/2.0 ipn/0.581 nodejs/10.16.0_LTS scratch-1d/1.1
alfred/0.1.17 eggnog-mapper/0.12.7 iqsub/1.0 nodejs/12.6.0 screen/4.6.2
allelecount/3.2.3 eggnog-mapper/0.99.3 iqtree/1.5.5 novocaller/20190521 scwrl/4.0
allelecount/3.3.1 eggnog-mapper/1.0.3 iqtree/1.6.1 novocraft/3.03.02 searchgui/2.8.5
:
/cm/local/modulefiles, in particular those highlighted above: tools, ngs, shared and use.own. These can be loaded using the using the command:
$ module load <module name>
module avail command.
$ module avail f
----------------------------------------------------------------------------------- /cm/local/modulefiles -----------------------------------------------------------------------------------
freeipmi/1.6.2
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/shared/modulefiles ----------------------------------------------------------------------
fftw2/openmpi/gcc/64/double/2.1.5 fftw2/openmpi/gcc/64/float/2.1.5 fftw3/openmpi/gcc/64/3.3.8
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/tools/modulefiles -----------------------------------------------------------------------
falcon/0.3.0 fastp/0.19.4 fasttree/2.1.8 fftw/3.3.6-pl1 firebird/CS/2.5.7.27050-0 flye/2.4.2 frogs/2.0.0
falcon/20160621 fastphylo/1.0.1 fasttree/2.1.9 fftw/3.3.6-pl2 firebird/SS/2.5.7.27050-0 foldx/4 frustratometer/2.0
falcon_zip/20180716 fastq-tools/0.8 fasttree/2.1.10 fftw/3.3.7 firefox/67.0 foldx/4_expires20190409 funannotate/1.1.1
famseq/1.0.3 fastqc/0.11.2 fastuniq/1.1 fftw/3.3.8 fithic/1.0.1 fpocket/3.1.2 funannotate/1.2.0
fasta/36.3.8e fastqc/0.11.4 fastx_toolkit/0.0.14(default) fgbio/0.8.1 fix_assembly_errors/20180508 fpocket/3.1.3 funannotate/1.3.2
fasta/36.3.8g fastqc/0.11.5 fchmm/1.0.0 fgbio/1.0.0 flash/1.2.11 fraggenescan/1.30 funannotate/1.3.4
fastani/1.1 fastqc/0.11.7 fdt/0.25 fgwas/0.3.6 flashpca/2.0 freebayes/1.0.2-33-gdbb6160 funannotate/1.5.1
fastme/2.1.5 fastqc/0.11.8 fdupes/1.6.1 figtree/1.4.4 fltk/1.3.3 freebayes/1.1.0-50-g61527c5 funannotate/1.6.0
fastml/3.1 fastqtl/2.184 feh/3.1 filezilla/3.44.2 fltk/1.3.4-2 freebayes/1.2.0-2-g29c4002 fuseq/1.1.2
fastNGSadmix/20190716 fastsimcoal/2.6.0.3 ffmpeg/4.1.3 find-clumpiness/0.2.3.1 fltk/1.3.5 freesasa/1.1 fusionmap/20150331
fastp/0.12.2 faststructure/20150319 fftw/3.3.4 fineradstructure/20180529 flye/2.3.7 freetype/2.9.1
module whatismodule whatis [modulefile...].
$ module whatis tools ngs gcc anaconda3/4.4.0
----------------------------------------------------------------------------------- /cm/local/modulefiles -----------------------------------------------------------------------------------
tools: Adds cached /services/tools modules
----------------------------------------------------------------------------------- /cm/local/modulefiles -----------------------------------------------------------------------------------
ngs: Adds cached NGS modules
----------------------------------------------------------------------------------- /cm/local/modulefiles -----------------------------------------------------------------------------------
gcc/8.2.0: adds GNU Cross Compilers to your environment variables
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/tools/modulefiles -----------------------------------------------------------------------
gcc/4.9.4: GCC 4.9.4 - GNU Compiler Collection
gcc/5.4.0: GCC 5.4.0 - GNU Compiler Collection
gcc/6.2.0: GCC 6.2.0 - GNU Compiler Collection
gcc/7.2.0: GCC 7.2.0 - GNU Compiler Collection
gcc/8.2.0: GCC 8.2.0 - GNU Compiler Collection
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/tools/modulefiles -----------------------------------------------------------------------
anaconda3/4.4.0: Anaconda3 4.4.0 - Python 3 distribution for scientific computing
module aproposmodule apropos <string>.This is the only module sub-command which currently does for case insensitive module parameter evaluation.
$ module apropos genome
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/tools/modulefiles -----------------------------------------------------------------------
agouti/0.3.3.1-gc8bd255: AGOUTI 0.3.3.1-gc8bd255 - Annotated Genome Optimization Using Transcriptome Information
allpathslg/52415: ALLPATHS-LG 52415 - short read genome assembler
allpathslg/52488: ALLPATHS-LG 52488 - short read genome assembler
anicalculator/1: ANIcalculator 1 - compute gANI,AF values between two genomes
arcs/1.0.0: ARCS 1.0.0 - Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data
arcs/1.1.0: ARCS 1.1.0 - Scaffold genome sequence assemblies using 10x Genomics data
argweaver/20150629: ARGweaver 20150629 - Sampling and manipulating genome-wide ancestral recombination graphs
ascatngs/4.2.1: ascatNgs 4.2.1 - Somatic copy number analysis using paired end wholegenome sequencing
baypass/2.1: BayPass 2.1 - Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables
bedops/2.4.14: BEDOPS 2.4.14 - fast, highly scalable and easily-parallelizable genome analysis toolkit
bedops/2.4.35: BEDOPS 2.4.35 - fast, highly scalable and easily-parallelizable genome analysis toolkit
bedtools/2.22.1: bedtools 2.22.1 - powerful toolset for genome arithmetic
bedtools/2.26.0: bedtools 2.26.0 - powerful toolset for genome arithmetic
bedtools/2.27.1: bedtools 2.27.1 - powerful toolset for genome arithmetic
bedtools/2.28.0: bedtools 2.28.0 - powerful toolset for genome arithmetic
bmagwa/1.0: BMAGWA 1.0 - Bayesian Model Averaging in Genome-wide Association Studies
bmagwa/2.0-20121210: BMAGWA 2.0-20121210 - Bayesian Model Averaging in Genome-wide Association Studies
bpga/1.3: BPGA 1.3 - tool for ultra-fast pan-genome analysis of microbes
brat_ng/20150505: BRAT NextGen 20150505 - Bayesian analysis of recombinations in whole-genome DNA sequence data
breakdancer/1.1_2011_02_21: BreakDancer 1.1_2011_02_21 - Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads
busco/3.0.1_20170529: BUSCO 3.0.1_20170529 - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
busco/3.0.2b_20170717: BUSCO 3.0.2b_20170717 - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
bwa/0.6.1: BWA 0.6.1 - Burrows-Wheeler Aligner, mapping low-divergent sequences against a large reference genome
bwa/0.7.6a-r433: BWA ExaScience 0.7.6a-r433 - Burrows-Wheeler Aligner (ExaScience fork), mapping low-divergent sequences against a large reference genome
bwa/0.7.10: BWA 0.7.10 - Burrows-Wheeler Aligner, mapping low-divergent sequences against a large reference genome
bwa/0.7.12: BWA 0.7.12 - Burrows-Wheeler Aligner, mapping low-divergent sequences against a large reference genome
bwa/0.7.15: BWA 0.7.15 - Burrows-Wheeler Aligner, mapping low-divergent sequences against a large reference genome
bwa/0.7.16a: BWA 0.7.16a - Burrows-Wheeler Aligner, mapping low-divergent sequences against a large reference genome
cbrc_last/861: CBRC LAST 861 - Genome-Scale Sequence Comparison
cbrc_last/963: CBRC LAST 963 - Genome-Scale Sequence Comparison
cdsgff2seq/20070813: cdsgff2seq 20070813 - read GFF, genome fasta; write CDS sequence, aa translation (with check for exon phase). write gene/exon offset subranges
clonalframeml/20170927: ClonalFrameML 20170927 - Efficient Inference of Recombination in Whole Bacterial Genomes
codingquarry/2.0: CodingQuarry 2.0 - highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
control-freec/11.5: Control-FREEC 11.5 - Copy number and genotype annotation in whole genome and whole exome sequencing data
cortex_var/1.0.5.21: cortex_var 1.0.5.21 - genome assembly and variation analysis from sequence data
das_tool/1.0: DAS_Tool 1.0 - Tool for genome-resolved metagenomics
das_tool/1.1.1: DAS_Tool 1.1.1 - Tool for genome-resolved metagenomics
disco/1.0: Disco 1.0 - Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler
discovar/52188: DISCOVAR 52188 - assemble genomes and find variants
discovar/52488: DISCOVAR 52488 - assemble genomes and find variants
discovardenovo/52488: DISCOVAR de novo 52488 - assemble genomes and find variants
discovarexp/52242: DISCOVAR de novo - assemble genomes and find variants
dissect/1.2: DISSECT 1.2 - massive genome analysis tool
eggnog-mapper/0.12.7: EggNOG-mapper 0.12.7 - Fast genome-wide functional annotation through orthology assignment
eggnog-mapper/0.99.3: EggNOG-mapper 0.99.3 - Fast genome-wide functional annotation through orthology assignment
eggnog-mapper/1.0.3: EggNOG-mapper 1.0.3 - Fast genome-wide functional annotation through orthology assignment
eggnog-mapper/20170307: EggNOG-mapper 20170307 - Fast genome-wide functional annotation through orthology assignment
estimate_genome_size.pl/0.05: estimate_genome_size.pl 0.05 - Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
module apropos
$ module apropos netMHC
---------------------------------------------------------------------- /cm/local/.modulefiles_cache/tools/modulefiles -----------------------------------------------------------------------
netmhc/3.0c: NetMHC 3.0c - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
netmhc/3.4a: NetMHC 3.4a - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
netmhc/4.0a: NetMHC 4.0a - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
netmhcii/2.3: NetMHCII 2.3 - predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles
netmhciipan/3.1a: NetMHCIIpan 3.1a - predicts binding of peptides to MHC class II molecules
netmhciipan/3.2: NetMHCIIpan 3.2 - predicts binding of peptides to MHC class II molecules
netmhcpan/2.8a: NetMHCpan 2.8a - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
netmhcpan/3.0a: NetMHCpan 3.0a - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
netmhcpan/4.0a: NetMHCpan 4.0a - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
$ module load netmhciipan/3.1a
module display module display [modulefile...].
$ module display RepeatMasker/4.0.6
-------------------------------------------------------------------
/cm/local/.modulefiles_cache/tools/modulefiles/RepeatMasker/4.0.6:
module-whatis {RepeatMasker 4.0.6 - screens DNA sequences for interspersed repeats and low complexity DNA sequences}
conflict RepeatMasker
prereq perl
prereq trf
prereq ncbi-rmblastn hmmer
prepend-path PATH /services/tools/RepeatMasker/4.0.6/util
prepend-path PATH /services/tools/RepeatMasker/4.0.6
prepend-path PERL5LIB /services/tools/RepeatMasker/4.0.6
setenv REPEATMASKER /services/tools/RepeatMasker/4.0.6
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library derived from Repbase sequences ) and Repbase, a service of the Genetic Information Research Institute.
-------------------------------------------------------------------
This command will also list
conflict (modules which conflict with this) and prereq (modules which must be loaded to use this).Listing software not included as modules
module display will inform you how you can find further information.Anaconda (python) packages
$ module display anaconda3/4.4.0
-------------------------------------------------------------------
/services/tools/modulefiles/anaconda3/4.4.0:
module-whatis anaconda3 4.4.0 - Python 2 distribution for scientific computing
conflict anaconda3
conflict anaconda
prepend-path PATH /services/tools/anaconda3/4.4.0/bin
prepend-path MANPATH /services/tools/anaconda3/4.4.0/share/man
prepend-path PYTHONPATH /services/tools/anaconda3/4.4.0/bin
prepend-path PYTHONPATH /services/tools/anaconda3/4.4.0/lib
prepend-path PYTHONPATH /services/tools/anaconda3/4.4.0/lib/python2.7
setenv ANACONDAHOME /services/tools/anaconda3/4.4.0
setenv QT_PLUGIN_PATH
To list currently installed Python packages, use command 'pip list' or 'pip list | grep -i <packagename>'
-------------------------------------------------------------------
$ module load anaconda3/4.4.0
$ pip list
Package Version Location
---------------------------------- ------------------- ------------------------------
-etworkx 2.4
-otocore 1.10.80
-penpyxl 2.6.2
-ytest 3.3.2
absl-py 0.7.1
adjustText 0.7.3
agate 1.6.1
agate-dbf 0.2.0
agate-excel 0.2.2
agate-sql 0.5.3
ago 0.0.9
aioeasywebdav 2.2.0
aiohttp 2.2.5
alabaster 0.7.10
albatradis x.y.z
alchy 2.2.2
alembic 1.0.11
altair 4.1.0
altgraph 0.15
anaconda-client 1.6.3
anaconda-navigator 1.6.2
anaconda-project 0.6.0
ansible 2.5.0
appdirs 1.4.3
apsw 3.9.2.post1
...
Perl-modules
$ module display perl/5.20.2
-------------------------------------------------------------------
/services/tools/modulefiles/perl/5.20.2:
module-whatis Perl 5.20.2 - highly capable, feature-rich programming language
conflict perl
conflict perl_LEGACY
prepend-path PATH /services/tools/perl/5.20.2/bin
prepend-path MANPATH /services/tools/perl/5.20.2/man
prepend-path PERL5LIB /services/tools/perl/5.20.2/lib/5.20.2
To list currently installed Perl modules, use command 'cpan -l'
-------------------------------------------------------------------
$ module load perl/5.20.2
$ cpan -l
arybase 0.07
Fcntl 1.11
re 0.26
NDBM_File 1.12
Socket 2.013
Opcode 1.27
B 1.48
POSIX 1.38_03
SDBM_File 1.11
Storable 2.49_01
Config 5.020002
DynaLoader 1.25
Cwd 3.48_01
...
R packages
$ module display R/3.2.5
-------------------------------------------------------------------
/services/tools/modulefiles/R/3.2.5:
module-whatis R 3.2.5 - software environment for statistical computing and graphics
conflict R
prereq gcc
prepend-path PATH /services/tools/R/3.2.5/bin
prepend-path MANPATH /services/tools/R/3.2.5/share/man
prepend-path LD_LIBRARY_PATH /services/tools/R/3.2.5/lib64/R/library
prepend-path LD_LIBRARY_PATH /services/tools/R/3.2.5/lib64/R/lib
prepend-path INCLUDE_PATH /services/tools/R/3.2.5/lib64/R/include
prepend-path CPATH /services/tools/R/3.2.5/lib64/R/include
prepend-path PKG_CONFIG_PATH /services/tools/R/3.2.5/lib64/pkgconfig
setenv RSCRIPTBINDIR /services/tools/R/3.2.5/bin
Use the following R commands to list installed packages:
> packinfo <- installed.packages()
> packinfo[,c("Package","Version")]
-------------------------------------------------------------------
$ module load gcc/5.2.0 R/3.2.5
$ R
> packinfo <- installed.packages()
> packinfo[,c("Package","Version")]
Package
abind "abind"
acepack "acepack"
ada "ada"
adabag "adabag"
ade4 "ade4"
AER "AER"
affxparser "affxparser"
...
Version
abind "1.4-5"
acepack "1.4.1"
ada "2.0-5"
adabag "4.1"
ade4 "1.7-5"
AER "1.2-5"
affxparser "1.42.0"
...
Using module output with other commands
module commands write their output to STDERR (where 'normal' commands write to STDOUT). So if you, for instance, use grep after a module command, the result might not be quite what you expected.
$ module load tools
$ module whatis | grep sequence
cluster-tools/7.0 : Adds cluster-tools to your environment
cmd : Adds the CMDaemon binaries to your path.
dot : adds `.' to your PATH environment variable
freeipmi/1.3.4 : adds FREEIPMI to your environment variables
ipmitool/1.8.13 : adds IPMItool to your environment variables
module-git : get this version of the module sources from SourceForge.net
module-info : returns all various module-info values
mvapich2/mlnx/gcc/64/2.0: adds MVAPICH2-gcc to your environment variables
ngs : adds NGS modules
null : does absolutely nothing
openldap : Adds the CMDaemon binaries to your path.
openmpi/mlnx/gcc/64/1.8.4rc1: adds OpenMPI to your environment variables
shared : adds shared modules
tools : adds /services/tools modules
use.own : adds your own modulefiles directory to MODULEPATH
version : Changes the MODULE_VERSION environment variable
acml/gcc/64/5.3.1 : adds ACML to your environment variables
acml/gcc/fma4/5.3.1 : adds ACML to your environment variables
acml/gcc/mp/64/5.3.1 : adds ACML to your environment variables
acml/gcc/mp/fma4/5.3.1: adds ACML to your environment variables
...list goes on and on and on...
You must remember to redirect STDERR (the
2>&1 below):
$ module whatis 2>&1 | grep sequence
FastTree/2.1.8 : FastTree 2.1.8 - A-M-L phylogenetic trees from alignments of nucleotide or protein sequences
RepeatMasker/4.0.5 : RepeatMasker 4.0.5 - screens DNA sequences for interspersed repeats and low complexity DNA sequences
beagle-lib/20150407 : BEAGLE 20150407 - general purpose library for evaluating the likelihood of sequence evolution on trees
bowtie2/2.2.4 : Bowtie 2 2.2.4 - ultrafast and memory-efficient aligning of sequencing reads to long reference sequences
bowtie2/2.2.5 : Bowtie 2 2.2.5 - ultrafast and memory-efficient aligning of sequencing reads to long reference sequences
bwa/0.7.10 : Burrows-Wheeler Aligner 0.7.10 - mapping low-divergent sequences against a large reference genome
bwa/0.7.12 : Burrows-Wheeler Aligner 0.7.12 - mapping low-divergent sequences against a large reference genome
cd-hit/4.5.4 : CD-HIT 4.5.4 - program for clustering and comparing protein or nucleotide sequences
cd-hit/4.6.1 : CD-HIT 4.6.1 - program for clustering and comparing protein or nucleotide sequences
hmmer/3.1b2 : HMMER 3.1b2 - biosequence analysis using profile hidden Markov models
interproscan/5.11-51.0: InterProScan 5.11-51.0 - scan protein and nucleic sequences against InterPro's signatures
ncbi-blast/2.2.30+ : BLAST 2.2.30+ - Basic Local Alignment Search Tool, finds regions of local similarity between sequences
sortmerna/2.0 : SortMeRNA 2.0 - biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads
trf/4.07b : Tandem Repeats Finder 4.07b - program to locate and display tandem repeats in DNA sequences
trinityrnaseq/2.0.6 : Trinity 2.0.6 - De novo Assembly of transcript sequences from Illumina RNA-Seq data
usearch/7.0.1090 : USEARCH 7.0.1090 - Ultra-fast sequence analysis with high-throughput search and clustering
usearch/8.0.1623 : USEARCH 8.0.1623 - Ultra-fast sequence analysis with high-throughput search and clustering
velvet/1.2.10 : Velvet 1.2.10 - sequence assembler for very short reads
vsearch/1.1.3 : VSEARCH 1.1.3 - multithreaded tool for processing metagenomic sequences
Adding and removing modules
module loadmodule load [modulefile...].tools) reference a new set of modulefiles, so if you for instance load tools and ngs modules, you will get access to a massive list of extra modulefiles.
$ module load tools ngs
$ module avail
...ignoring parts of listing for readability...
--------------------------------------------------- /cm/local/.modulefiles_cache/modulefiles ----------------------------------------------------
anaconda3/2.1.0 hdf5/1.10.0 plink2/1.90beta3
anaconda3/2.2.0 hdf5/1.8.15p1 plumed/2.2.1
anaconda3/4.4.0 hisat2/2.0.1-beta polysolver/1.0
anaconda3/2.1.0 hkl2map/0.3.i-beta poppler/0.45.0
anaconda3/2.2.0 hlaminer/1.3 pplacer/1.1.alpha17
anaconda3/4.4.0 hlareporter/1.0.3 prank/140603
anarci/1.0 hla-vbseq/20150729 preseq/1.0.2
annovar/2015jun17 hmmer/2.3.2 price/1.2
ansys/16.2 hmmer/3.1b2 prinseq-lite/0.20.4
ansys/17.0 htslib/1.2.1 prodigal/2.6.2
ansys/17.1 htslib/1.3.1 progressivecactus/20160427
apache-maven/3.3.3 idba/1.1.1(default) prokka/1.11
...long listing left out...
------------------------------------------------- /cm/local/.modulefiles_cache/ngs/modulefiles --------------------------------------------------
bcl2fastq/2.17.1.14 ncbi-blast/2.2.26 SPAdes/3.7.0
bedtools/2.22.1(default) ncbi-blast/2.2.30+ SPAdes/3.8.0
bwa/0.7.10(default) ncbi-blast/2.2.31+ sratoolkit/2.4.5-2
circos/0.64 ncbi-tools/current(default) sratoolkit/2.5.7
circos/0.67-7(default) netmhciipan/3.1a srnaworkbench/4.0-alpha
circos-tools/0.21 netmhcpan/2.8a srnaworkbench/4.1-alpha
cope/1.2.5 netsurfp/1.0b ssake/3.8.3
cufflinks/2.2.1 ngsqctoolkit/2.3.3 tabix/0.2.6
ensembl-tools/78(default) PBSuite/15.2.20 tabix/1.2.1(default)
express/1.5.1 pear/0.9.6 trf/4.07b
...long listing left out...
gcc/4.8.2) reference a particular version of a tool.
Generally, it is recommended to always include the version when loading a tool; if you do not specify version, the (default) will be loaded if any is available - otherwise the command will print an error.
$ module load gcc
$ which gcc
/cm/shared/apps/gcc/4.8.2/bin/gcc
$ module load anaconda3/2.1.0
$ which python
/services/tools/anaconda-2.1.0/bin/python
conflict and missing prereq
$ module load RepeatMasker/4.0.6
RepeatMasker/4.0.6(37):ERROR:151: Module 'RepeatMasker/4.0.6' depends on one of the module(s) 'perl/5.8.9 perl/5.20.2 perl/5.20.1'
RepeatMasker/4.0.6(37):ERROR:102: Tcl command execution failed: prereq perl
module display command for further information.
$ module display RepeatMasker/4.0.6
-------------------------------------------------------------------
/services/tools/modulefiles/RepeatMasker/4.0.6:
module-whatis RepeatMasker 4.0.6 - screens DNA sequences for interspersed repeats and low complexity DNA sequences
conflict RepeatMasker
prereq perl
prereq trf
prereq ncbi-rmblastn
prepend-path PATH /services/tools/RepeatMasker/4.0.6
prepend-path PERL5LIB /services/tools/RepeatMasker/4.0.6
-------------------------------------------------------------------
module list
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools 3) ngs 4) anaconda3/2.1.0
module switchswitch [modulefile1] modulefile2
If modulefile1 is not specified, then it is assumed to be the currently loaded module with the same root name as modulefile2.
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools 3) ngs 4) anaconda3/2.1.0
$ module switch anaconda3/2.1.0 anaconda3/4.4.0
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools 3) ngs 4) anaconda3/4.4.0
$ module switch anaconda3/2.2.0
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools 3) ngs 4) anaconda3/2.2.0
$ module switch anaconda3/2.2.0 perl/5.20.2
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools 3) ngs 4) perl/5.20.2
module unloadmodule unload [modulefile...]
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools 3) ngs 4) perl/5.20.2
$ module unload perl ngs
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2 2) tools
$ module purge
$ module list
No Modulefiles Currently Loaded.
Managing modules in your login environment
You should keep the number of modules that you load in your login environment to an absolute minimum, usually limited to only tools and/or ngs.
Having too many modules loaded can potentially cause problems with pre-requirements and/or conflicts, affecting or even breaking your environment.module init... family of commands.Use <tab>-completion to list the sub-commands:
$ module init<tab><tab>
initadd initclear initlist initprepend initrm initswitch
initadd modulefile...
$ man module
Modules in batch jobs
With permanent module settings described above submit a batch job with standard `qsub` command.
First add anaconda2/2.2.0 (which includes Python 2.7) to your login environment:
$ module initadd tools anaconda2/2.2.0
Start a new login shell to activate the updated environment, and run your script:
$ qsub script.py
with an example `script.py`::
#!/usr/bin/env python from ase import Hartree print Hartree
You can also enable the required modules for a given batch job (depending on the shell this may work only when permanent modules settings related to those modules are NOT present in you shell startup scripts).
This feature is useful mostly for developers when comparing different versions of a code, or for making sure that a given software will be used during the whole computational project.
Examples are given below:
Create the following `myscript.sh` script::
#!/bin/sh module load tools module load anaconda2/2.2.0 # For Python 2.7 module load unison module load ncbi-blast python script.py
You submit this script with::
$ qsub myscript.sh
Modules in Perl
With our standard Perl, module load tools perl, we have included a PM Env::Modulecmd that provides an automated interfaces to the module command directly from inside Perl scripts.
Using personal modules
The recommended place to keep personal modules is under
~/privatemodules. To enable this directory use the following command::$ module load use.own
and to disable it::
$ module unload use.own
Computerome provides commented templates in directory /services/tools/modulefiles/.template_simple/.
Please read the online Man page of MODULEFILE for further information.
Requesting software
To request installation of new software (or other version of existing software), please send a mail from your department mail to Computerome support - preferably including a descriptive subject line, incl. tool name, and information on where the requested software can be obtained (Home-page, download information, etc.):
Subject: Software request - NewBrilliantTool
Hi, I would like to use NewBrilliantTool on Computerome, it is available from: http://<some_url>/software/NewBrilliantTool
User installed software
Individual users can also install own software in their Project (for sharing inside the project) or HOME (for strictly personal use) directory.
This is only recommended for software that is actively being developed or maintained at Computerome.
Regular software should preferably be available through the standard modules structure.
Regular software should preferably be available through the standard modules structure.
Tips and Tricks
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