Fix reference customization - #148
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Requires #147 to be merged first though. |
jonasfreimuth
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Techincally git-lfs is the right thing for including the large files, but currently this is causing to many issues. The references can be expected to not change much so this should be ok.
Else the env cannot be created when channel prio is strict.
To ensure this is usable by everyone.
Now we can import script modules in tests.
I will add unit tests, so this is more descriptive.
For reproducible conda envs.
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Else test fails might not be discovered when they happen, or at all.
So partial genotyping does not depend on previous whole allele output.
Ensures tests are independent & more reproducible.
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More idiomatic, also clearer.
Where they should live for other tests to use them.
Should lead to the script actually running.
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For individually unit testing customization code with debug support.
As far as I can tell these are leftovers from debugging.
This is git, if we need it we can reintroduce it.
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Hello everyone,
than you very much for providing this fine immunogenomics tool! I would like to integrate the quantification step into my pipeline, but currently the reference customization appears to be broken. Even running
arcasHLA customize --helpresults in the following error:The issue seems that the current arcasHLA dependencies use a new
biopythonversion in whichBio.Alphabetis deprecated. However, as far as I can tell, thegeneric_dnaobject is never used anywhere. So by simply removing that import, the customization should be possible again.I have already done that on my own fork and managed to get
customizeandquantto run again.