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BruneauLab-GladstoneInstitutes / computing-envs

Docker and Singularity files for single cell analysis
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pyvcf==0.6.8 installation fails #5

Open h836472 opened 2 years ago

h836472 commented 2 years ago

Dear Developers,

Monocle3 build from docker file keeps failing. Latest error happens at pip3 install pyvcf==0.6.8- Output: Downloading PyVCF-0.6.8.tar.gz (34 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [1 lines of output] error in PyVCF setup command: use_2to3 is invalid. [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details.

h836472 commented 2 years ago

this looks like a setuptools sysntax incompatibility issue. I am trying to overcome it with adding pip3 install setuptools==58 right above