samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Version: 1.2

Added: February, 2015

Link: http://samtools.sourceforge.net/

Show all available versions of samtools

module avail samtools

Load samtools module:

module load samtools/1.2

clone samtools repo & compile it

git clone git@github.com:samtools/htslib.git
git clone git@github.com:samtools/samtools.git
cd samtools
git checkout 1.2
sudo mkdir -p /export/apps/samtools/1.2/
sudo chown joguya:joguya /export/apps/samtools/1.2/
make
make prefix=/export/apps/samtools/1.2/ install
sudo chown -R root:root /export/apps/samtools/1.2/

samtools module file

#%Module1.0
#####################################################################
##
## samtools Modulefile
## by James Oguya <j.oguya@cgiar.org>
## February, 2015
##

set appname         samtools
set version         1.2
set prefix          /export/apps/${appname}/${version}
set exec_prefix     ${prefix}/bin
set datarootdir     ${prefix}/share
set url "http://samtools.sourceforge.net"
set msg "This module adds samtools v$version to various paths\n\nsamtools Official Site: $url\n"

proc ModulesHelp { } {
    puts stderr "$msg"
}

module-whatis   "$msg"

conflict        samtools

prepend-path    PATH        ${exec_prefix}
prepend-path    MANPATH     ${datarootdir}/man

deploy the new module using ansible

ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules