Hello!
According the README, I should install PyVCF:
conda install -c bioconda pyvcf
But PyVCF is deprecated for python3. It is impossible to install it without tricks...
Step 67/78 : RUN pip3 install --no-cache-dir --upgrade pyfaidx pyvcf
---> Running in 9c616c689149
Collecting pyfaidx
Downloading pyfaidx-0.6.4.tar.gz (100 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 KB 1.3 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting pyvcf
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.
WARNING: You are using pip version 22.0.4; however, version 22.1 is available.
You should consider upgrading via the '/usr/bin/python -m pip install --upgrade pip' command.
The command '/bin/sh -c pip3 install --no-cache-dir --upgrade pyfaidx pyvcf' returned a non-zero code: 1
Hello! According the README, I should install PyVCF:
But PyVCF is deprecated for python3. It is impossible to install it without tricks...
Upd: this is dublicate of https://github.com/ylab-hi/ScanNeo/issues/10