KneadData setup.py update to URL reference for TRF.exe

Feature/Pull Request Feature/Pull Request
1

In the GitHub repository for KneadData, the setup.py script references two URLs for retrieving the TRF executable download on lines #246 & 248 (shown below).

trf_exe = “trf”

if mac_os:
    url = "http://tandem.bu.edu/trf/downloads/trf409.macosx"
else:
    url = "http://tandem.bu.edu/trf/downloads/trf409.linux64"

Those links aren’t valid anymore. The website appears to have been updated and the TRF executables were moved to GitHub (GitHub - Benson-Genomics-Lab/TRF at v4.09.1).

As such, the setup.py file needs to be updated because it causes a TRF “not found” error.

Also of note, this error appears (different verbiage, but same sentiment) if you try to use PIP install kneaddata and then run the kneaddata command as well - I’m not sure where that error is being generated from.

I submitted a pull request for the change on GitHub if you could please review it and/or modify as necessary.