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dePamphilis / PlantTribes

PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics
GNU General Public License v3.0
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Various pipeline fixes #7

Closed gregvonkuster closed 7 years ago

gregvonkuster commented 7 years ago

@ewafula This PR include the following fixes

I'll perform more in-depth testing and get back to you shortly.

ewafula commented 7 years ago

Sure, Greg. Thanks!

On Thu, Feb 16, 2017 at 9:11 AM Greg Von Kuster notifications@github.com wrote:

@ewafula https://github.com/ewafula This PR include the following fixes

  • typo bug fixes for each of the pipelines intriduced yesterday
  • Added missing cap3 and hmmsearch entries in the plantTribes.config needed by the AssemblyPostPorcesser pipeline
  • Added your pasta enhancement for error checking to another appropriate code section in the PhylogenomicsAnalysis pipeline.

I'll perform more in-depth testing and get back to you shortly.

You can view, comment on, or merge this pull request online at:

https://github.com/dePamphilis/PlantTribes/pull/7 Commit Summary

  • Various pipeline fixes

File Changes

Patch Links:

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gregvonkuster commented 7 years ago

@ewafula Please merge this and the additional PRs I will be submitting, but don't create another release tag until we're done with the PRs. Thanks!

gregvonkuster commented 7 years ago

@ewafula My 2nd commit adds subroutines for creating new directory during pipeline runs, allowing for creating the directory only if it does not yet exist. This fixes issues I encountered with the PhylogenomicsAnalysis pipeline when attempting to create multiple sequences and phylo trees. In some scenarios the required directories had not been created.

gregvonkuster commented 7 years ago

@ewafula I am not able to get pasta to work successfully. I'm now getting this error from the command line.

PASTA ERROR: PASTA is exiting because of an error:
'/home/_conda/envs/__plant_tribes_phylogenomics_analysis@_uv_/lib/python2.7/site-packages/PASTA-1.6.4-py2.7.egg/bin/mafft' not found. Please install 'mafft' and/or configure its location correctly in '/home/.pasta/pasta_tool_paths.cfg'

I'm considering eliminating the pasta option temporarily from the Galaxy tool wrapper for the PhylogenomicsAnalysis pipeline until we can figure out if we can make it work.

gregvonkuster commented 7 years ago

@ewafula I've completed my testing and I believe that with these 2 commits you can create another tagged release from which we can build. Thanks!

ewafula commented 7 years ago

Greg, PRs merged and v0.6 released.

On Thu, Feb 16, 2017 at 11:22 AM, Greg Von Kuster notifications@github.com wrote:

@ewafula https://github.com/ewafula I've completed my testing and I believe that with these 2 commits you can create another tagged release from which we can build. Thanks!

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gregvonkuster commented 7 years ago

Awesome! Thanks a bunch @ewafula ;) I will submit new conda recipes for this version of the pipelines this afternoon.