Struggling with pysam intallation using conda prompt

[RONNY ISRAEL GONGORA JAMA]

I can' install pysam. I followed up the installation step in its Github repository:

conda config --add channels defaults 

conda config --add channels 

conda-forge conda config --add channels bioconda 

conda install pysam  

 And then, these messages appeared:

********************************************************

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-32

  - https://conda.anaconda.org/bioconda/noarch

  - https://conda.anaconda.org/r/win-32

  - https://conda.anaconda.org/r/noarch

  - https://conda.anaconda.org/conda-forge/win-32

  - https://conda.anaconda.org/conda-forge/noarch

  - https://repo.anaconda.com/pkgs/main/win-32

  - https://repo.anaconda.com/pkgs/main/noarch

  - https://repo.anaconda.com/pkgs/r/win-32

  - https://repo.anaconda.com/pkgs/r/noarch

  - https://repo.anaconda.com/pkgs/msys2/win-32

  - https://repo.anaconda.com/pkgs/msys2/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.

******************************************

What am I supposed to do?

I using Anaconda 32 bits

[Peter Cock]

On Wed, Nov 11, 2020 at 3:21 AM RONNY ISRAEL GONGORA JAMA
<rigo...@espe.edu.ec> wrote:
>
> I can' install pysam. I followed up the installation step in its Github repository:
>
> conda config --add channels defaults
> conda config --add channels
> conda-forge conda config --add channels bioconda
> conda install pysam

I'm assuming there was a line break problem, and you actually ran
these four commands:

conda config --add channels defaults

conda config --add channels conda-forge

conda config --add channels bioconda

conda install pysam

That ought to have found pysam from bioconda:

https://anaconda.org/bioconda/pysam

However, I have bad news for you. You are using Windows, and bioconda
does not currently package anything for Windows - just Linux and
macOS. You can see that in the list of packages they have for pysam:

https://anaconda.org/bioconda/pysam/files

Conda itself, and conda-forge, do cover Windows though.

Peter

[GONGORA JAMA, RONNY ISRAEL]

I agree with you, I'm starting with python programming and I just realized that yesterday. Thanks for the confirmation!

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[Sujay Ayyagari]

Hey there, I am trying to do the same thing and the same errors are being shown for me too. Was the installation of pysam on conda successful for you. I tried everything and still nothing works

[Peter Cock]

Hello Sujay,

Which operating system are you using? As I said to Ronny, unfortunately
BioConda currently only supports Linux and macOS - although Conda itself,
and conda-forge, do cover Windows.

If you are on Windows, you will have to install samtools without using conda.

Peter

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