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chapmanb / cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
http://cloudbiolinux.org
MIT License
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bismark_indices.loc missing #318

Closed gcampanella closed 5 years ago

gcampanella commented 5 years ago

This is related to PRs #313 (which added Bismark to ngs_pipeline_minimal), #316 and #317 (which added GGD recipes for the one-time genome preparation step required by Bismark).

In 1e09aed0bd7a35bf02bee2e75c2b4dd1dbfa4b53 I added some lines to galaxy.py hoping that bismark_indices.loc would be generated automatically, but this doesn't seem to be the case.

I'm not sure I understand how *.loc file are created. If you could point me in the right direction, I'd be happy to work on another PR to fix this.

chapmanb commented 5 years ago

Gianluca; Thanks much for working on this and sorry about the many places to adjust to add new indices. There are quite a few different ways to do it that developed historically, so a few places to adjust. I've added in the bits to point at the output directory from your GGD directories which I hope will get the indexes created correctly for you. Please let us know if you hit any other issues.

gcampanella commented 5 years ago

That's great, thanks so much @chapmanb! :slightly_smiling_face: