updates the loftee plugin #44
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| gnupg2 \ | ||
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Can't see if it's just reformatted/reodered or a package added here?
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ah yeah, this was just splitting the packages out and ordering alphabetically - no changes
vladsavelyev
approved these changes
Oct 19, 2022
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I'm going to merge/build this, and if it works well I'll look into the CI fixes (also broken on main, and I'm reluctant to change the working build) |
vladsavelyev
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The
mainbranch of loftee causes a ton of error logging messages when running on GRCh38.Example here (similar errors being throw 27000+ times during processing of one variant subset)
There is a separate branch which we can use instead, with an updated version of the plugin files, see konradjk/loftee#84 (and other similar issues)
The path to copy the plugin files to contains a
*-This copy works for both situations when building the image, but doesn't resolve hard-coding like this
As of today I don't believe there's a way to set an env variable to the result of a RUN command, otherwise this could be used:
ls -l ${MAMBA_ROOT_PREFIX}/share/ | grep ensembl | awk '{ print $9}'this could be used in setting the path in the production-pipelines job?
... but this looks really heavy handed