Pysam installation error through conda on linux env

[Aditya Garg]

Hi,

I am trying to install pysam using the following commands on Linux VM

conda config --add channels r

conda config --add channels bioconda

conda install pysam

I get the following error

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.

This can take several minutes.  Press CTRL-C to abort.

failed                                                                        

 

UnsatisfiableError: The following specifications were found to be incompatible with each other:

 

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

 

  - feature:/linux-64::__glibc==2.31=0

  - feature:|@/linux-64::__glibc==2.31=0

  - pysam -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

 

Your installed version is: 2.31

What does this error mean and how would I be able to install pysam?

[Marcel Martin]

Hi Adita,

On 11/09/2021 01.27, Aditya Garg wrote:
> I am trying to install pysam using the following commands on Linux VM
>
> conda config --add channels r
> conda config --add channels bioconda

You should also adad the "conda-forge" channel as recommended in the
Bioconda installation instructions because you’ll get an outdated pysam
version otherwise.

> conda install pysam
>
> I get the following error

[...]> UnsatisfiableError: The following specifications were found to be
> incompatible with each other:
[...]

> What does this error mean and how would I be able to install pysam?

I am not 100% sure, but I would guess that this occurs because some
other previously installed package has conflicting requirements.

You should be able to avoid this by installing pysam into a separate
Conda environment:

conda create -n myenv pysam

This will a) create the "myenv" environment and b) install pysam into
it. Then you need to activate the environment with

conda activate myenv

After that, any "conda install" etc. will affect only the activated
environment. You need to do the activation step every time you want to
use the packages installed into it, but the advantage is that you can
have separate environments for separate projects, and that you can very
easily delete an environment and start over when there is a problem.

If adding "conda-forge" and using a separate environment doesn’t help,
you should send us the output of "conda info".

Regards,
Marcel