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transdecoder-software

TransDecoder

  • TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

v2.0.1

Usage

  • Show all available versions of TransDecoder
    module avail TransDecoder
  • Load TransDecoder module:
    module load TransDecoder/2.0.1

Installation

  • clone TransDecoder repo & compile it
    git clone git@github.com:TransDecoder/TransDecoder.git
    git checkout 2.0.1
    make
    sudo mkdir -p /export/apps/TransDecoder/2.0.1/
    sudo cp -r . /export/apps/TransDecoder/2.0.1/
  • TransDecoder module file
    #%Module1.0
    #####################################################################
    ##
    ## TransDecoder Modulefile
    ## By James Oguya, j.oguya@cgiar.org
    ## February, 2015
    ##
    
    set appname             TransDecoder
    set version             2.0.1
    set prefix              /export/apps/${appname}/${version}
    set exec_prefix_util    ${prefix}/util
    set exec_prefix_bin     ${exec_prefix_util}/bin
    
    set url "http://transdecoder.github.io/"
    set msg "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.\nTransDecoder Official Site: $url\n"
    
    module-whatis $msg
    
    proc ModulesHelp { } {
        puts stderr "$msg"
    }
    
    conflict        TransDecoder
    
    prepend-path    PATH    ${prefix}
    prepend-path    PATH    ${exec_prefix_util}
    prepend-path    PATH    ${exec_prefix_bin}
  • deploy the new module using ansible
    ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules
transdecoder-software.txt · Last modified: 2015/02/11 14:39 by joguya