• Each directory should contain the following structure

  • Script.sh (This should be renamed to something that is intuitive)

    • This should be the only script in this directory
    • Running this script without options (or -h) should display an infromative usage statement with clear descriptions of all variables
    • Any optional arguments that are needed in ancillary scripts must be captured here

  • scripts/

    • Any script that is needed to support the primary wrapper should be placed here

  • images/

    • This is where you should put any images you need for this website
    • We may want to rename this to be outputs so that we can keep example output files

  • config/

  • Should contain at least 1 file named config.cfg

  • This is where you should define all of the tool paths necessary to run all the script

    • An example would look like this:

              JAVA_PATH=/biotools/biotools/java/jdk1.7.0_72/bin
              BEDTOOLS_PATH=/usr/local/biotools/bedtools/2.20.1/bin
              VCFLIB_PATH=/usr/local/biotools/vcflib/2015_3_20/bin
              GATK_PATH=/biotools/biotools/gatk/3.3.0
              REF_GENOME=/dlmp/misc-data/reference/ggpsReferences/genomes/withMT/hs37d5.chr.fa
              R_PATH=/usr/local/biotools/r/3.1.1/bin