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platanus-software

Platanus

  • Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples.
  • First, it constructs contigs using the algorithm based on de Bruijn graph.
  • Second, the order of contigs is determined according to paired-end (mate-pair) data and constructs scaffolds.
  • Finally, paired-end reads localized on gaps in scaffolds are assembled and gaps are closed.

Platanus/1.2.1

Usage

  • Show all versions of platanus
    $ module avail platanus
    
    ---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
    platanus/1.2.1
  • Load a specific version
    $ module load platanus/1.2.1
  • Show help
    $ platanus --help
    platanus --help 
    
    Platanus version: 1.2.1
    Usage: platanus Command [options]
    
    Command: assemble, scaffold, gap_close

Installation

  • platanus comes already compiled, so all you have to do is unzip & copy to export-apps
    mkdir ~/src/platanus
    cd ~/src/platanus
    wget http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201/platanus
    chmod +x platanus
    sudo mkdir -p /export/apps/platanus/1.2.1/
    sudo cp platanus /export/apps/platanus/1.2.1/
  • Create module file & push to github repo
    #%Module1.0
    #####################################################################
    ##
    ## Platanus Modulefile
    ## By James Oguya, j.oguya@cgiar.org
    ## November, 2014
    ##
    
    set appname         platanus
    set version         1.2.1
    set prefix          /export/apps/${appname}/${version}
    set exec_prefix     ${prefix}
    set url "http://platanus.bio.titech.ac.jp/platanus-assembler/platanus-1-2-1/"
    set msg "Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples.\nPlatanus Official Site: $url\n"
    
    module-whatis $msg
    
    proc ModulesHelp { } {
        puts stderr "$msg"
    }
    
    conflict        platanus
    
    prepend-path    PATH    ${exec_prefix}
  • Clone repo on all compute nodes using ansible
    ansible-playbook compute.yml --limit=compute --tags=modules -K
platanus-software.txt · Last modified: 2014/11/14 15:45 by joguya