Open jkalleberg opened 3 years ago
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?
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!
@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
When installing
hap.py
via Conda,rtg-tools
is not a dependency for thehap.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 ifrtg-tools
was included as a dependency in the BioCondahap.py
package for use with thevcfeval
engine.