danielecook
commented
4 years ago @danrlu there are a couple of things you an try. Quest has weird networking issues.
1.) Try swapping ftp for http in the URL.
2.) Try using curl instead of wget or use wget with the -L option.
3.) If all else fails download locally and upload...the files are not that big.
Once you have this setup please close this issue as I have added the script to scripts/setup_genome.sh. Thanks!
When I was running wi-nf on Quest, all the ftp step failed to fetch and I couldn't figure out how to fix it. The fetch would work if running on terminal, but would fail when called within the pipeline. It may be a Quest setting issue, but it's probably more robust to download files outside of the workflow, and use the local files.