- 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