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Software installed on Computerome

At Computerome we maintain en 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 Login to Computerome.



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 definitions are contained in so-called modulefiles located in several directories. The directory structure is dependent on the system.

Modules are activated by default for users on Computerome.

Listing and finding modules

Computerome utilities for modules

To help in finding tools, we have created a module 'computerome_utils' with a handful of small utilities - currently (2019.01.19):
moduleavail <string>
moduleapropos [-i] <string>
modulewhatis <string>
findintools [-i] <string>
findinanaconda [-i] <string>
findinperl [-i] <string>
findinr [-i] <string>

Just load it and try it out

$ module load tools computerome_utils/1.0

module avail

To list your currently available modules, type:

$ module avail


The command will per default list something similar to this:

------------------------------------------------------ /cm/local/modulefiles -------------------------------------------------------
cluster-tools/7.0            ipmitool/1.8.13              ngs                          shared
cmd                          module-git                   null                         tools
dot                          module-info                  openldap                     use.own
freeipmi/1.3.4               mvapich2/mlnx/gcc/64/2.0     openmpi/mlnx/gcc/64/1.8.4rc1 version

------------------------------------------------------ /cm/local/.modulefiles_cache/shared/modulefiles ------------------------------------------------------
acml/gcc/64/5.3.1                              intel/compiler/64/14.0/2013_sp1.3.174
acml/gcc/fma4/5.3.1                            intel/mkl/64/11.1/2013_sp1.3.174
acml/gcc/mp/64/5.3.1                           intel-cluster-checker/2.2.1
acml/gcc/mp/fma4/5.3.1                         intel-cluster-runtime/ia32/3.7
acml/gcc-int64/64/5.3.1                        intel-cluster-runtime/intel64/3.7
acml/gcc-int64/fma4/5.3.1                      intel-cluster-runtime/mic/3.7
acml/gcc-int64/mp/64/5.3.1                     intel-mpi/32/4.1.3/049
acml/gcc-int64/mp/fma4/5.3.1                   intel-mpi/64/4.1.3/049
acml/open64/64/5.3.1                           intel-mpi/mic/4.1.3/049
acml/open64/fma4/5.3.1                         intel-tbb-oss/ia32/43_20141023oss
acml/open64/mp/64/5.3.1                        intel-tbb-oss/intel64/43_20141023oss
acml/open64/mp/fma4/5.3.1                      iozone/3_420
acml/open64-int64/64/5.3.1                     lapack/gcc/64/3.5.0
acml/open64-int64/fma4/5.3.1                   lapack/open64/64/3.5.0
acml/open64-int64/mp/64/5.3.1                  moab/7.2.9-2014091216-96b8ec34-b9-EL6(default)
acml/open64-int64/mp/fma4/5.3.1                moab/7.2.9.h2-2014092308-42354522-b30-EL6
blacs/openmpi/gcc/64/1.1patch03                mpich/ge/gcc/64/3.1
blacs/openmpi/open64/64/1.1patch03             mpich/ge/open64/64/3.1
blas/gcc/64/1                                  mpiexec/0.84_432
blas/open64/64/1                               mvapich/gcc/64/1.2rc1
bonnie++/1.97.1                                mvapich/open64/64/1.2rc1
cmgui/7.0                                      mvapich2/gcc/64/2.0b
default-environment                            mvapich2/open64/64/2.0b
fftw2/openmpi/gcc/64/double/2.1.5              netcdf/gcc/64/4.3.1.1
fftw2/openmpi/gcc/64/float/2.1.5               netcdf/open64/64/4.3.1.1
fftw2/openmpi/open64/64/double/2.1.5           netperf/2.6.0
fftw2/openmpi/open64/64/float/2.1.5            open64/4.5.2.1
fftw3/openmpi/gcc/64/3.3.3                     openblas/dynamic/0.2.8
fftw3/openmpi/open64/64/3.3.3                  openmpi/gcc/64/1.8.1
gcc/4.8.2                                      openmpi/open64/64/1.8.1
globalarrays/openmpi/gcc/64/5.3                pbspro/12.2.1.140292
globalarrays/openmpi/open64/64/5.3             scalapack/gcc/64/1.8.0
hdf5/1.6.10                                    scalapack/open64/64/1.8.0
hdf5_18/1.8.12                                 sge/2011.11p1
hpl/2.1                                        slurm/14.03.0
hwloc/1.8.1                                    torque/4.2.9


Regular users should focus on modules located under /cm/local/modulefiles, in particular those highlighted above: toolsngs, shared and use.own. These can be loaded using the using the command:

$ module load <module name>

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 module avail command.

$ module avail f

------------------------------------------------------ /cm/local/modulefiles -------------------------------------------------------
freeipmi/1.3.4

------------------------------------------------------ /cm/local/.modulefiles_cache/shared/modulefiles ------------------------------------------------------
fftw2/openmpi/gcc/64/double/2.1.5    fftw2/openmpi/open64/64/double/2.1.5 fftw3/openmpi/gcc/64/3.3.3
fftw2/openmpi/gcc/64/float/2.1.5     fftw2/openmpi/open64/64/float/2.1.5  fftw3/openmpi/open64/64/3.3.3

module whatis

To get basic information on the modulefiles, you can use module whatis [modulefile...]

$ module whatis tools ngs use.own gcc/4.8.4 torque anaconda2/2.2.0
tools                : adds /services/tools modules
ngs                  : adds NGS modules
use.own              : adds your own modulefiles directory to MODULEPATH
gcc/4.8.4            : adds GNU Cross Compilers to your environment variables
torque               : TORQUE 5.1.1.h1 - Resource Manager
anaconda2/2.2.0      : Anaconda 2.2.0 - Python 2 distribution for scientific computing

module apropos

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 supports the -i flag for case insensitive module parameter evaluation.
$ module apropos -i genome
L_RNA_scaffolder/20130610: L_RNA_Scaffolder 20130610 - scaffolding tool using long trancriptome reads to scaffold genome fragments
SOAPdenovo/2.04-r240 : SOAPdenovo2 2.04-r240 - Large-size genome de-novo assembler
SPAdes/3.5.0         : SPAdes 3.5.0 - genome assembler
allpathslg/52488     : ALLPATHS-LG 52488 - short read genome assembler
bedtools/2.22.1      : BEDTools Suite 2.22.1 - powerful toolset for genome arithmetic
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
discovar/52188       : DISCOVAR 52188 - assemble genomes and find variants
discovarexp/52242    : DISCOVAR de novo - assemble genomes and find variants
gcta/1.24.4          : GCTA 1.24.4 - Genome-wide Complex Trait Analysis
gemma/0.94.1         : GEMMA 0.94.1 - software implementing the Genome-wide Efficient Mixed Model Association algorithm
gwimpcompss/0.9.6    : GWImp-COMPSs 0.9.6 - Integrated Framework for Large-scale Genome-wide Imputation and Association Testing
kentUtils/311        : kentUtils 311 - UCSC Genome Browser and Blat utilities
maker/2.31.8         : Maker 2.31.8 - portable and easily configurable genome annotation pipeline
mutect/1.1.7         : MuTect 1.1.7 - method for reliable and accurate identification of somatic point mutations in NGS data of cancer genomes
plink/1.07           : PLINK 1.07 - whole genome association analysis toolset
plink2/1.90beta3     : PLINK2 1.90beta3 - upgraded whole genome association analysis toolset
ray/2.3.1            : Ray 2.3.1 - parallel de novo genome assembler using MPI
satsuma/3.0          : Satsuma 3.0 - highly parallelized program for high-sensitivity, genome-wide synteny
sga/0.10.13          : SGA 0.10.13 - de novo genome string graph assembler
smalt/0.7.6          : SMALT 0.7.6 - efficiently aligns DNA sequencing reads with a reference genome
snptest/2.5          : SNPTEST 2.5 - program for the analysis of single SNP association in genome-wide studies
tabix/0.2.6          : tabix 0.2.6 - Generic indexer for TAB-delimited genome position files

Example using module apropos

$ module apropos -i netMHC
netmhc/3.0c          : NetMHC 3.0c - Prediction of peptide-MHC class I binding using artificial neural networks (ANNs)
netmhciipan/3.1a     : netMHCIIpan 3.1a - predicts binding of peptides to MHC class II molecules
netmhcpan/2.8a       : netMHCpan 2.8a - predicts binding of peptides to any known MHC molecule using artificial neural networks
$ module load netmhciipan/3.1a

module display

Further information is available with module display [modulefile...].

$ 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 also list conflict (modules which conflict with this) and prereq (modules which must be loaded to use this).

Listing software not included as modules

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) packagesPerl-modules, and R packages. In these cases, module display will inform you how you can find further information.

Anaconda (python) packages

$ module display anaconda2/4.0.0
-------------------------------------------------------------------
/services/tools/modulefiles/anaconda2/4.0.0:

module-whatis    Anaconda2 4.0.0 - Python 2 distribution for scientific computing
conflict         anaconda2
conflict         anaconda
prepend-path     PATH /services/tools/anaconda2/4.0.0/bin
prepend-path     MANPATH /services/tools/anaconda2/4.0.0/share/man
prepend-path     PYTHONPATH /services/tools/anaconda2/4.0.0/bin
prepend-path     PYTHONPATH /services/tools/anaconda2/4.0.0/lib
prepend-path     PYTHONPATH /services/tools/anaconda2/4.0.0/lib/python2.7
setenv           ANACONDAHOME /services/tools/anaconda2/4.0.0
setenv           QT_PLUGIN_PATH

To list currently installed Python packages, use command 'conda list' or 'conda list <modulename>'
-------------------------------------------------------------------

$ module load anaconda2/4.0.0
$ conda list
# packages in environment at /services/tools/anaconda2/4.0.0:
#
alabaster                 0.7.9                     <pip>
alabaster                 0.7.9                    py27_0
alchy                     2.2.2                     <pip>
anaconda                  custom                   py27_0
anaconda-client           1.4.0                    py27_0
anaconda-navigator        1.1.0                    py27_0
anvio                     2.0.2                     <pip>
appdirs                   1.4.0                     <pip>
argcomplete               1.0.0                    py27_1
argh                      0.26.2                   py27_0    bioconda
argh                      0.26.2                    <pip>
...

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 load

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 ----------------------------------------------------
anaconda2/2.1.0                    hdf5/1.10.0                        plink2/1.90beta3
anaconda2/2.2.0                    hdf5/1.8.15p1                      plumed/2.2.1
anaconda2/4.0.0                    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
anaconda3/4.0.0                    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 anaconda2/2.1.0
$ which python
/services/tools/anaconda-2.1.0/bin/python

Modules 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
-------------------------------------------------------------------

module list

Verify which modules are loaded

$ module list
Currently Loaded Modulefiles:
  1) gcc/4.8.2        2) tools            3) ngs              4) anaconda2/2.1.0

module switch

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) anaconda2/2.1.0
$ module switch anaconda2/2.1.0 anaconda3/4.0.0
$ module list
Currently Loaded Modulefiles:
  1) gcc/4.8.2        2) tools            3) ngs              4) anaconda3/4.0.0
$ 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 unload

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

module purge

In case all modules need to be unloaded at once use:

$ 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 moabtorquetools 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 <tab>-completion to list the sub-commands:
$ module init<tab><tab>
initadd      initclear    initlist     initprepend  initrm       initswitch


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



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/CBS.
Regular software should preferably be available through the standard modules structure.




Tips and Tricks

How to connect to CBS MySQL server from Computerome

Contact information: Peter Wad Sackett, CBS, pws@cbs.dtu.dk

Please read the document How to connect to CBS MySQL server from Computerome, if you need to have access to the CBS datawarehouse solution from Computerome.

Note: You need to have a CBS account to use this guide.