samtools-software
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samtools
- samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
v1.2
- Version: 1.2
- Added: February, 2015
Usage
- Show all available versions of samtools
module avail samtools
- Load samtools module:
module load samtools/1.2
Installation
- 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
samtools-software.1423740141.txt.gz · Last modified: 2015/02/12 11:22 by joguya