“The Environment Modules package provides for the dynamic modification of a user’s environment via modulefiles.
Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the environment can be modified on a per-module basis using the module command which interprets modulefiles. Typically modulefiles instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. modulefiles may be shared by many users on a system and users may have their own collection to supplement or replace the shared modulefiles.
Modules can be loaded and unloaded dynamically and atomically, in an clean fashion. All popular shells are supported, including bash, ksh, zsh, sh, csh, tcsh, as well as some scripting languages such as perl.
Modules are useful in managing different versions of applications. Modules can also be bundled into metamodules that will load an entire suite of different applications.” [1]
As stated before the environment package can be used in several popular shells. Before you can use modules you must initialize it.
Initialize modules for the bash shell:
# . /usr/modules/init/bashYou can use the module command to list the available modules on a system, load/unload, and show the modules that you currently have loaded. To list the available modules use the ‘avail’ option:
List all the modules available on a system (note that this list is not current):
benji@fortyfour ~ $ module avail
---------------------------------------------- /opt/modules/modulefiles ----------------------------------------------
R/2.15.3 hmmer/4.0 parsinsert/1.04(default)
R/3.0.2 hyphy/2.1.2(default) partitionfinder/1.1.1(default)
R/3.1.0(default) ima2/8.27.12(default) paup/4.10(default)
arc/1.0 infernal/1.0.2 pcap/1.0
arc/1.1(default) infernal/1.1(default) perl/5.18.0(default)
arc-dev/1.0 java/1.6.0 phredphrap/0.990329(default)
arc-dev/1.1(default) java/1.7.0(default) phylip/3.695(default)
avida/2.12.4(default) jmodeltest/2.1.3 phyml/3.0(default)
beast/1.7.5 jmodeltest/2.1.4(default) phyml/3.0-20120412
beast/1.8.0(default) lamarc/2.1.8(default) phyml/dev
blat/35(default) libncl/2.1.18(default) pplacer/1.1
blat-fastq/35(default) mafft/7.046 prank/1.0(default)
boost/1.55.0 mafft/7.050 prokka/1.10(default)
bowtie2/2.1.0(default) mafft/7.130(default) prokka/1.9
cap3/2013-08-06(default) migrate/3.6(default) prottest/3.4-20140123(default)
cdbtools/1.0(default) mlcoalsim/1.42(default) python/2.7.3
cdhit/4.5.4 mothur/1.25.0 python/2.7.5(default)
cdhit/4.6.1(default) mothur/1.30.2(default) python/3.3.2
chimeraslayer/2010-04-29(default) mrbayes/3.2.1(default) qiime/1.8.0(default)
clann/3.2.3(default) mummer/3.23(default) raxml/7.2.8
clearcut/1.0.9(default) muscle/3.8.31(default) raxml/7.3.0
clustalo/1.2.0(default) ncbi/2.2.28 raxml/8.0.4(default)
clustalw/2.1(default) ncbi-blast/2.2.28(default) rdp_classifier/2.2(default)
cmake/2.8.11.1(default) ncbi-blast-legacy/2.2.22(default) repeatmasker/4.0.3
cufflinks/2.1.1(default) ncbi-c-toolkit/20120212(default) repeatmasker/4.0.5(default)
dotur/1.53(default) ncbi-toolkit/12_0_0 roche454/2.6
emboss/6.5.7(default) ncl/2.1.18(default) roche454/2.8
faststructure/1.0(default) omssa/2.1.9 roche454/2.9(default)
fasttree/2.1.3 openmpi/1.6.4 rtax/0.984(default)
fasttree/2.1.7(default) openmpi-apps/1.6.4/abyss/1.3.6 stacks/1.12
fastx/0.0.13.2(default) openmpi-apps/1.6.4/blast/1.6.0 stacks/1.20(default)
fiji/1.0(default) openmpi-apps/1.6.4/clustalw/0.13 structure/2.3.4(default)
flash/1.2.9(default) openmpi-apps/1.6.4/examl/2.04 tax2tree/1.0
fusionq/0.5(default) openmpi-apps/1.6.4/garli/2.01 tbl2asn/1.44(default)
garli/2.01(default) openmpi-apps/1.6.4/gromacs/4.6.3 treemix/1.12(default)
gcc/4.3.3(default) openmpi-apps/1.6.4/migrate/3.6 treepl/1.0(default)
grc/1.0(default) openmpi-apps/1.6.4/mothur/1.30.2 trf/4.07b(default)
grc/2.0 openmpi-apps/1.6.4/mrbayes/3.2.1 uclust/1.2.22(default)
gsl/1.16(default) openmpi-apps/1.6.4/raxml/7.7.6 usearch/5.2.236(default)
hmmer/3.0 openmpi-apps/1.6.4/raxml/8.0.5 velvet/1.1(default)
hmmer/3.1 paml/4.7(default)
hmmer/3.1b1(default) parallel/20131022(default)To see what a specific module is use the whatis command with modules.
benji@fortyfour ~ $ module whatis ncbi
ncbi : Adds both the ncbi-blast and ncbi-c-toolkit to your environment
ncbi : NCBI BLAST is a search tool for genetic sequencesYou can get a list of all the environment manipulations that a specific module sets, including the actual paths.
benji@fortyfour ~ $ module show ncbi
-------------------------------------------------------------------
/opt/modules/modulefiles/ncbi/2.2.28:
module-whatis Adds both the ncbi-blast and ncbi-c-toolkit to your environment
module-whatis NCBI BLAST is a search tool for genetic sequences
module load ncbi-c-toolkit
module load ncbi-blast
-------------------------------------------------------------------To obtain a list of the modules you have loaded use the ‘list’ command.
benji@fortyfour ~ $ module list
No Modulefiles Currently Loaded.
benji@fortyfour ~ $ module load R
benji@fortyfour ~ $ module list
Currently Loaded Modulefiles:
1) R/3.1.0Loading a module to customize your environment is easy using the load command.
Load the python module:
benji@fortyfour ~ $ module load python
benji@fortyfour ~ $ module list
Currently Loaded Modulefiles:
1) R/3.1.0 2) python/2.7.5To remove a module from your environment use the ‘unload’ command
Unload the R module:
benji@fortyfour ~ $ module unload R
benji@fortyfour ~ $ module list
Currently Loaded Modulefiles:
1) python/2.7.5To unload all modules, use the purge command
benji@fortyfour ~ $ module purge
benji@fortyfour ~ $ module list
No Modulefiles Currently Loaded.