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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Checkqc recipe / Illumina-interop not working ? #36828

Open apeltzer opened 1 year ago

apeltzer commented 1 year ago

Dear all,

we've been trying to use the checkqc container on quay.io that was created from the checkqc recipe and receive an error about interop not being installed properly:

File "/usr/local/lib/python3.10/site-packages/checkQC/handlers/error_rate_handler.py", line 3, in <module>
    from checkQC.parsers.interop_parser import InteropParser
  File "/usr/local/lib/python3.10/site-packages/checkQC/parsers/interop_parser.py", line 4, in <module>
    from interop import py_interop_run_metrics, py_interop_run, py_interop_summary
ModuleNotFoundError: No module named 'interop'

However, interop seems to be installed as also listed in the run part of the checkqc recipe:

root@4d8d487c7200:/data/run1# find / -name "interop" -type d
/usr/local/interop
/usr/local/interop/include/interop
/usr/local/interop/share/illumina/interop

Any idea what might be the issue here? @cbrueffer maybe?

cbrueffer commented 1 year ago

I haven't used this software in a while, but I just tried the Bioconda version (not the container), and it produced the same error. I don't have much time to look into it at the moment, perhaps next week.