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Hisat2 Python 3.x package broken #20942

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epruesse opened this issue Mar 17, 2020 · 0 comments
Open

Hisat2 Python 3.x package broken #20942

epruesse opened this issue Mar 17, 2020 · 0 comments

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@epruesse
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This was enabled in #19100 following discussion in #18911. Alas, there are no tests verifying that it actually does, and it is currently broken.

Specifically, the code in hisat2_read_stats.py is not python 3 compatible and the script will run futilely through the entire fq file, not ever finding line[0] == '@' because line is bytes, not str and thus line[0] is int not chr.

ping @ewels

Unless I am mistaken, conda still silently uses old builds to satisfy dependencies. So we cannot just require py2k again, but will have to fix the package. Either 2to3 isn't working, or it's not being run.

@bgruening Have there been changes to marking packages as broken? As in, is there a way to tell the solver to not use them without removing them from the repo? The py36 and py37 packages we have at the moment are 100% useless.

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