PyVCF

[sandain]

Hi. I'm following the directions for installation that you have in your README, and I'm having an issue installing the PyVCF prerequisite.

$ conda install -c bioconda pyvcf
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.                                                                                  failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - pyvcf -> python[version='2.7.*|3.4.*|3.5.*|3.6.*']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - python=3.7 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.17

I was able to get all other prerequisite packages installed. Upon further investigation, it appears that PyVCF is no longer maintained. However, there appears to be a new fork that is being maintained. I installed this using pip install PyVCF3. Hopefully this works.

[dolittle007]

Thank you so much for your suggestions.

Have you tried using pip install pyvcf to install PyVCF? Or you may try mamba to install the prerequisite packages. Native conda is not good at solving dependency conflicts. You can install mamba in conda environment, then use mamba to install packages. Mamba is way better than conda in terms of dependency solving and efficiency.

I don't know whether PyVCF3 has the same API as PyVCF. If it is true, it is okay to install PyVCF3 instead of PyVCF.
I will check it out and modify the code if necessary.
Thank you again.

[serge2016]

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

[serge2016]

@dolittle007 pip3 install pyvcf doesn't work...
Is this package necessary? This package is dead for about a year...