ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data
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PyVCF is deprecated for python3 #14

Closed serge2016 closed 2 years ago

serge2016 commented 2 years ago

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

Upd: this is dublicate of https://github.com/ylab-hi/ScanNeo/issues/10