Cannot install `vatools` with pip

[famosab]

I created a new conda environment on my linux workstateion running Rocky Linux 9.3 (Blue Onyx) with python 3.12 and installed pip.

Running pip install vatools leads to

Collecting vatools
  Using cached vatools-5.1.1-py3-none-any.whl.metadata (813 bytes)
Collecting vcfpy==0.12.3 (from vatools)
  Using cached vcfpy-0.12.3.tar.gz (1.0 MB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      ERROR: Can not execute `setup.py` since setuptools is not available in the build environment.
      [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

Are there any hints on what I missied here? Installing other packages via pip works fine.

[susannasiebert]

The error Can not execute setup.py since setuptools is not available in the build environment. seems to indicate that you don't have setuptools installed, which seems strange. Do you have setuptools installed and if so, what version is installed?

[famosab]

This is all the packages found in the conda environment:

# packages in environment at /home/paifb01/mambaforge/envs/pvac:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.45.1               h2797004_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
openssl                   3.2.1                hd590300_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
python                    3.12.1          hab00c5b_1_cpython    conda-forge
readline                  8.2                  h8228510_1    conda-forge
setuptools                58.0.0                   pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge

So I have setuptools version 58

[famosab]

Update: When I set the Python version to 3.8 the installation works.

[susannasiebert]

I'm glad you were able to install VAtools on python 3.8. The setuptools version in your 3.12 container seems to be quite old. Can you try upgrading it and see if that changes the behavior?

[famosab]

I actually downgraded it because the lates version did not work either and that was something that I encountered with other tools sometimes.

[cedarice]

I thought the installation failed because the version of the vcfpy package is too old.

[famosab]

We also have the issue that the exact required version of vcfpy is not available on bioconda anymore:
https://anaconda.org/channels/bioconda/packages/vcfpy/overview