stacks

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

• Version: 1.24
• Added: February, 2015
• Link: http://creskolab.uoregon.edu/stacks/manual/

• Show all available versions of stacks

  module avail stacks

• Load stacks module:

  module load stacks/1.24

• download stacks tarball & compile it

  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/

• stacks module file

  #%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

• deploy the new module using ansible

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