====== stacks ======
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.

==== v1.24 ====
  * Version: 1.24
  * Added: February, 2015
  * Link: http://creskolab.uoregon.edu/stacks/manual/

=== Usage ===
  * Show all available versions of stacks<code>module avail stacks</code>
  * Load stacks module: <code>module load stacks/1.24</code>

=== Installation ===
  * download stacks tarball & compile it<code>wget http://creskolab.uoregon.edu/stacks/source/stacks-1.24.tar.gz -O stacks-1.24.tar.gz
tar -xvf stacks-1.24.tar.gz
cd stacks-1.24/
sudo mkdir -p /export/apps/stacks/1.24/
sudo chown -R joguya:joguya /export/apps/stacks/1.24/
./configure --prefix=/export/apps/stacks/1.24/ --enable-bam --with-bam-include-path=/export/apps/samtools/0.1.19/include/bam --with-bam-lib-path=/export/apps/samtools/0.1.19/lib
make
make install
sudo chown -R root:root /export/apps/stacks/1.24/</code>
  * stacks module file<code>#%Module1.0
#####################################################################
##
## stacks Modulefile
## By James Oguya, j.oguya@cgiar.org
## February, 2015
##

set appname         stacks
set version         1.24
set prefix          /export/apps/${appname}/${version}
set exec_prefix     ${prefix}
set url "http://creskolab.uoregon.edu/stacks/manual/"
set msg "a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.\Stacks Official Site: $url\n"

module-whatis $msg

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

conflict        stacks

prepend-path    PATH    ${exec_prefix}/bin
</code>

  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules</code>