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rsem-software

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RSEM

  • RSEM(RNA-Seq by Expectation-Maximization) is an accurate quantification of gene and isoform expression from RNA-Seq data.

v1.2.9

Usage

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

Installation

  • clone RSEM repo & compile it
    git clone https://github.com/bli25wisc/RSEM.git
    cd RSEM
    git checkout v1.2.9
    module load bowtie2/2.2.3 bowtie/1.1.1
    make
    sudo mkdir -p /export/apps/RSEM/1.2.9/
    sudo cp -r . /export/apps/RSEM/1.2.9/
  • RSEM module file
    #%Module1.0
    #####################################################################
    ##
    ## RSEM Modulefile
    ## By James Oguya, j.oguya@cgiar.org
    ## February, 2015
    ##
    
    set appname         RSEM
    set version         1.2.9
    set prefix          /export/apps/${appname}/${version}
    set exec_prefix     ${prefix}
    set url "http://deweylab.biostat.wisc.edu/rsem/"
    set msg "RSEM(RNA-Seq by Expectation-Maximization): accurate quantification of gene and isoform expression from RNA-Seq data.\nRSEM Official Site: $url\n"
    
    module-whatis "$msg"
    
    proc ModulesHelp { } {
        puts stderr "$msg"
    }
    
    conflict        RSEM
    
    prepend-path    PATH    ${exec_prefix}
    
    # load RSEM dependencies - bowtie2/2.2.3, bowtie/1.1.1, R/3.1.0
    if { ! [is-loaded bowtie2/2.2.3] } {
        module load bowtie2/2.2.3
    }
    
    if { ![is-loaded bowtie/1.1.1] } {
        module load bowtie/1.1.1
    }
    
    if { ![is-loaded R/3.1.0] } {
        module load R/3.1.0
    }
  • deploy the new module using ansible
    ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules
rsem-software.1423654471.txt.gz · Last modified: 2015/02/11 14:34 by joguya