Bioconda Package Install Bug

[jkalleberg]

When installing hap.py via Conda, rtg-tools is not a dependency for the hap.py package and requires additional installation steps. While the manual install/build notes mention using the --with-rtg-tools flag, this would be a lot easier if rtg-tools was included as a dependency in the BioConda hap.py package for use with the vcfeval engine.

[nate-d-olson]

You can run hap.py using --engine=vcfeval if you have rtg-tools=3.10.1 bioconda package installed in the same environment, e.g. https://github.com/snakemake/snakemake-wrappers/blob/master/bio/hap.py/hap.py/environment.yaml. I'll let @mbargull, from the Bioconda team, chime in about adding rtg-tools to the hap.py bioconda package?

[jkalleberg]

Hello, thank you. I ended up rebuilding my environment to include rtg-tools. I did have a follow-up question: was there a particular reason v0.3.15 was removed from BioConda? I am currently using that version, but when I went to the package files bioconda to show someone else, the most current release was no longer available.

Was there a bug in the upgrade to rtg-tools version 3.12.1? Should I downgrade my environment? If you have an alternate reason for removing it, please let me know. TIA!

[nate-d-olson]

@jkalleberg Sorry for the slow response. I think the current rtg-tools version works. Previously versions after rtg tools 3.10.1 were not compatible. However, I ran happy following conda env file (below), which using rtg 3.1.2.1 without error. So the issue has apparently been addressed.

channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - hap.py ==0.3.14
  - rtg-tools ==3.12.1