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flash-software

FLASH

FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

v1.2.11

Usage

  • Show all available versions of flash
    module avail flash
  • Load flash module:
    module load flash/1.2.11
  • get quick help:
    flash --help

Installation

  • Download flash src tarball, extract it & compile it
    wget "http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.11.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fflashpage%2F&ts=1418712841&use_mirror=tenet" -O FLASH-1.2.11.tar.gz
    tar -xvf FLASH-1.2.11.tar.gz
    cd FLASH-1.2.11
    make
    sudo mkdir -p /export/apps/FLASH/1.2.11
    sudo cp flash /export/apps/FLASH/1.2.11/
  • flash module file
    #%Module1.0
    #####################################################################
    ##
    ## FLASH Modulefile
    ## By James Oguya, j.oguya@cgiar.org
    ## December, 2014
    ##
    
    set appname         FLASH
    set version         1.2.11
    set prefix          /export/apps/${appname}/${version}
    set exec_prefix     ${prefix}
    set url "http://sourceforge.net/projects/flashpage/"
    set msg "FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies..\nFLASH Official Site: $url\n"
    
    module-whatis $msg
    
    proc ModulesHelp { } {
        puts stderr "$msg"
    }
    
    conflict        FLASH
    
    prepend-path    PATH    ${exec_prefix}
  • deploy the new module using ansible
    ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=module
flash-software.txt · Last modified: 2014/12/16 12:19 by joguya