Software
Created: 16-03-2022 07:12:50 by Computerome
Updated: 24-03-2025 14:02:16 by Computerome
Introduction
An extensive and ever-growing list of software and scientific tools are available to Computerome. The software and the tools are preconfigured and ready to use and updated on demand.
Currently more than 4.500 tools are installed and available on Computerome, and new tools are continuously installed and made available to the users. Should a user require specific tools not already on Computerome, we will do our best to make it available.
Currently, this service is only available for CentOS supported software tools. Windows based software tools can be provided as an extra service.
Standard software and tools installed and delivered on Computerome are provided on free, open source or academic licensing terms, and the Computerome team provides software tool installation, maintenance, and upgrades services of the portfolio of tools on demand.
Please note, that commercial use of software tools may require special agreements with the licence owner, and it is the responsibility of the user to ensure compliance with the license owner’s conditions for commercial use of the software.
Note:
This document is about the tools that you would like us to install for you, if you would like to know about how to install tools for yourself, you can check the link below:
https://www.computerome.dk/wiki/installing-and-managing-your-own-software-modules-in-hpc
Module Environment Guide
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 definitions are contained in so-called modulefiles located in several directories. The directory structure is dependent on the system you are working on (HPC , SPC, etc.). Modules are activated by default for users on Computerome.
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 (Software Request), including the tool name, and information on where the requested software can be obtained (homepage, download information, etc.).
User installed software
Individual users can also install own developed software in their Project (for sharing inside the project) or HOME (for strictly personal use) directories. This is only recommended for software that is either actively being developed or maintained at Computerome, or where license terms prevent installation and use through the shared Environment Module system.
Installed software
Regular software should preferably be available through the standard modules structure.
To help in finding tools, we have created a module computerome_utils
with a handful of small utilities.
$ module load tools computerome_utils/2.0
Module Utils Tools
moduleavail <string>
list available environment 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 packages
To list your currently available modules, type the command below:
$ module avail
The command will per default list something similar to this:
$ 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
Regular users should focus on modules located under /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>
where 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 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
To get basic information on the modulefiles, you can use module 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
To search for a particular string in the basic information on the modulefiles, you can use module 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
Example using 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
Further information about specific modules is available with module display [modulefile...]
This command will also list conflict
(modules which conflict with this) and prereq
(modules which must be loaded to use this).
$ 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.
-------------------------------------------------------------------
To add one or more modules, use module load [modulefile...]
. Modules listed without version information (like 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...
Modules listed with version information (like 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
modules load
will report any 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
If you get such a message, you can use 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
-------------------------------------------------------------------
This command will verify which modules are loaded
$ module list
Currently Loaded Modulefiles:
1) gcc/4.8.2
2) tools
3) ngs
4) anaconda3/2.1.0
To switch loaded modulefile1
with modulefile2
, use switch[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
To remove one or more modules, use module 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
In case all modules need to be unloaded at once use this commmand
$ module purge
$ module list
No Modulefiles Currently Loaded.
RStudio Server
On this page we are going to explain how you can use RStudio Server and how you can load the modules inside RStudio Server environment. The following RStudio Server versions and R versions are available:
- RStudio 1.4.1717 with R version 4.1.0
- RStudio 2022.07.02-576 with R version 4.2.0
First you need to login to Computerome. Once you are logged in you need to get an interactive node as you are not allowed to run your jobs on the login node, you can check on the following page how you can get an interactive node.
To confirm you are working in an interactive node, when you get the prompt at the interactive node, you will be able to see the node’s name:
[user_name@g-01-c0015 ~] $
In this example, “g-01-c0015” is the name of the node, your node name will differ. If you have customised your prompt to not include the hostname, you can also run the “hostname” command to view the name of the mode.
Now that you have your interactive node it is time to load RStudio Server module. You have to load module tools first and then you are able to load RStudio Server Module
For RStudio 1.4.1717 with R version 4.1.0
$ module load tools
module load rstudio-server/1.4.1717
For RStudio 2022.07.02-576 with R version 4.2.0
$ module load tools
module load rstudio-server/2022.07.2-576
Now that you have loaded the module you are able to run the following commands and based on the R version that you need you can choose which one you want to run. After you have run one of the above commands it will take several seconds and then if RStudio Server is installed successfully you will see the following message and it means you can go to the next step.
For RStudio 1.4.1717 with R version 4.1.0
rstudio1.4.1717-R.4.1.0-install
For RStudio 2022.07.02-576 with R version 4.2.0
rstudio2022.07.2-576-R.4.2.0-install
The message after RStudio Server is successfully installed:
********************************* Rstudio-Server is running now ********************************
Please follow https://www.computerome.dk/display/C2W/Rstudio+Server to find out the instructions
*****************PLEASE BE AWARE THAT THIS MODULE ONLY WORKS ON COMPUTEROME CLUSTER NOT ON THE CLOUDS*********************
if you need rstudio-server to be running on your cloud please contact computerome@dtu.dk
But if you see the below message it means RStudio Server has not been installed correctly and you need to contact us
--------------------Something went wrong please contact computerome@dtu.dk---------------------
*****************PLEASE BE AWARE THAT THIS MODULE ONLY WORKS ON COMPUTEROME CLUSTER NOT ON THE CLOUDS*********************
if you need rstudio-server to be running on your cloud please contact computerome@dtu.dk
Now that you have RStudio Server up and running the next step is to create a tunnel to your interactive node over Computerome login node, in order to do that you leave the current terminal open and then you open a new terminal and run the following commands to create the tunnel
ssh -L 8787:<your_interactive_node_name>:8787 <username>@ssh.computerome.dk
You will be prompted to enter your Computerome password. After entering your password and passing the two factor authentication step, you open a browser in your computer (Firefox, Chrome, Safari) and then you open this website
http://localhost:8787
You can use your Computerome username and password to login and begin to work with RStudio Server. If you need any of the Computerome modules (such as anaconda, Cuda, etc) to be available on your RStudio Server, you will have to load them inside your R environment, if you need anaconda3/2020.07 to be loaded on your R environment you can run the below commands. You can change anaconda3/2020.07 with any module that you wish to have on your R environment.
library("RenvModule")
module("load", "tools")
module("load", "anaconda3/2020.07")
Tips and Tricks
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, 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 ' -------------------------------------------------------------------
$ 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" ...
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
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. It is possible to permanently add, manipulate and remove
modules in your login environment, by using the module init...
family of
commands.
Use completion to list the sub-commands:
$ module init
initadd
initclear
initlist
initprepend
initrm
initswitch
Command | Description |
---|---|
initadd modulefile... |
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
$ man module
You can 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.
Create the following `myscript.sh` script:
#!/bin/sh
module load tools
module load anaconda3/4.4.0
module load unison
module load ncbi-blast
python script.py
With our standard Perl, module load tools perl
, we have included a
PM command that provides an automated interface to the module
command directly from inside Perl scripts.
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 <a href="http://modules.sourceforge.net/man/modulefile.html"rel="nofollow">Man page of MODULEFILE for further information.
Reference Databases
Computerome provides access to a collection read-only reference databases related to bioinformatics and the life sciences.
Note: The reference databases are provided as is and was last updated late 2020.
If you need newer or different data you MUST provide your own!
$ /home/databases
$ ls
1000genomes gemini ncbi
alphafold genomics-public-data ncbi-blast
annovar gnomad_data nr
bio_databank gtdbtk nr_tnpe
bioinf_db gunc nt
blastdb HPE_WP15 nt_tnpe
cat humann2 oncotator
_CBSREADME ihmp oncotator_v1_ds_Jan262014
centrifuge intact orthodb
cgepipeline kegg pfam
CheckM kegg.old rgtdata
ctat_resource_lib kraken rgtdata_OLD
dalilite kraken2 rRNA_databases
datax kronatools samsa2
ebi ku-cbd sanger
eggnog-mapper mariadb
ensembl81 mariadb.recover test
ensembl81.txt meme tipp
fataydatabase metagenomics variant_effect_predictor
funannotate metasnv virsorter
gatk-legacy-bundles midas