README.md

pgdspider_scripts

these are scripts that will help you run pgdspider from the command line

for converting an ima file from rad_haplotyper, goto the ima2arlequin dir

How To

1. Identify the pgd*.bash file you want to run
2. Manually edit that pgd*.bash file to have the right file paths
3. Review the matching *.spid file to be sure it's doning what you wnat it to.
4. Run that bash script you just manually edited and give the input file as an argument.

pgdSCRIPT.bash infile

Adding to this dir

If the conversion you want to do doesn't have a bash script or spid here, you can either run pgdspider as it was intended, or contribute to this directory.

To contribute:

1. Make the spid file using the pgdspider GUI, follow the naming conventions in other *.spid here
2. Look at the *.spid to see the official name given to the file formats you are converting from and to
3. make a copy of the most similar exising pgd*bash script and rename it following the format of the other scripts
4. update the variables in your pgd*bash, don't forgot to update the variable pointing to the *.spid file
5. run pgd*.bash
6. if successful, push the changes to this repo