Installing Pysam....

[J]

I followed the instructions on the github, and I receive the following error:

(pysam) PS D:\projects\dragen\git\dls-pgx-bioinfo-scripts> conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top
 - bioconda
 - conda-forge
 - defaults
 - r
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: failed

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

  - pysam

Current channels:

  - https://conda.anaconda.org/bioconda
  - https://conda.anaconda.org/conda-forge
  - defaults
  - https://conda.anaconda.org/r

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.

---

what am I doing wrong?

[OSPython]

I have the same issue. 

I searched Bioconda for 'pysam' packages. No matches are found.

conda search pysam --channel bioconda
Loading channels: done
No match found for: pysam.

Then, I cloned the pysam GitHub repository and tried installing it using PIP. That was not successful either.

d:\python\pysam>pip install .
Processing d:\python\pysam
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  ERROR: Command errored out with exit status 1:

[John Marshall]

On April 20, 2024, OSPython <osma...@gmail.com> wrote:

I have the same issue. 

I searched Bioconda for 'pysam' packages. No matches are found.

Bioconda does not support Windows.

Then, I cloned the pysam GitHub repository and tried installing it using PIP. That was not successful either.

d:\python\pysam>pip install .

At present, compiling pysam on Windows will require some effort. This will improve at some point (see [1]) but it will still be a while before that lands.

    John

[1] https://github.com/pysam-developers/pysam/pull/1274

[teepean47]

At the moment pysam works only when compiled with MinGW using MSYS2 shell so it won't be appearing at PyPi as they seem to only support MSVC as a compiler. As for Bioconda they do not support Windows. " NOTE: Bioconda supports only Linux (64-bit and AArch64) and macOS (x86_64)"