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stacks-software

stacks

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

v1.24

Usage

  • Show all available versions of stacks
    module avail stacks
  • Load stacks module:
    module load stacks/1.24

Installation

  • 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
stacks-software.txt · Last modified: 2015/02/10 14:44 by joguya