Unable to pip install pysam on Windows

[dino945]

Hi, I try to do "pip install pysam" in Windows 10 using python 3.7.9.
Here is the error message return:

Anyone that has clue on this error?

[aryarm]

yes, I had issues like these back when v0.19.1 was released b/c wheels hadn't been uploaded for that release

unfortunately, I'm now getting different installation issues with v0.20.0 because an sdist hasn't been uploaded for that release

is there any chance the pysam team can upload an sdist for v0.20.0?

[AndreasHeger]

Ah, will check. I managed to time the last pysam release with a pypi downtime window.

[AndreasHeger]

@aryarm, I have uploaded the tar-ball. Apologies for the over-sight.
@dino945 , sorry I am not familiar with windows. Have you tried wsl?

[aryarm]

thank you so much, @AndreasHeger !

[pnrobinson]

Hi @AndreasHeger -- we are getting the following error on an M1 Mac

pip install pysam
(...)
 File "/private/var/folders/6q/nqfsh3cs775bb1rnrs7n_c_htypxv6/T/pip-install-i1h3zu3z/pysam_9d9c611018f741b7a603d298a813e761/cy_build.py", line 69, in build_extension
          relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
                                                                 ~~~~~~~~~~~~~~~~~^^^^^^
      KeyError: 'SO'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pysam

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

Any ideas how to fix this?

[jmarshall]

@pnrobinson: That is #1154, which has already been fixed on the master branch.

[pnrobinson]

@jmarshall thanks -- so does this mean I need to install from a local clone of the master branch (pip install still does not work)?

[jmarshall]

@pnrobinson: At present you would need to install from a Git repository. A new release which will contain this fix is imminent and will of course be installable via pip.

[snowformatics]

Hi,

I am having the same problem as @dino945 on Windows 10 and Python 3.7. is it possible to install pysam on Windows?

Thanks

[yzliu01]

Same problem as here on Win10 Python 3.10 with pip 23.0.1. It's very strange.
Cannot install using conda either, even this package is there. It seems to be the same issue as I had for vcfpy, which it could be only installed using git clone file.

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install pysam
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pysam

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch
  - https://conda.anaconda.org/r/win-64
  - https://conda.anaconda.org/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

also for

conda install -c bioconda pysam
conda install -c "bioconda/label/cf201901" pysam

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pysam

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch
  - https://conda.anaconda.org/r/win-64
  - https://conda.anaconda.org/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

[teepean]

Pysam would require some major patching to start working on Windows. There is an old PR that used to work but I haven't been able to compile any recent versions.

#964