pbsim2 on bioconda

[nick-youngblut]

I see pbsim is on bioconda. Any plans to also add pbsim2?

[idfarbanecha]

Hello @nick-youngblut, I am not a pbsim2 developer, but I added the latest version (2.0.1) to bioconda.

[sinamajidian]

It seems that it has some conflicts with even a fresh conda env

$ conda install -c bioconda pbsim2
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.                                                     failed

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

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:
python=3.9 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']
python=3.9 -> libgcc-ng[version='>=7.3.0']
pbsim2 -> libgcc-ng[version='>=9.3.0']

and also with python 3.8

Package libgcc-ng conflicts for:
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']
pbsim2 -> libgcc-ng[version='>=9.3.0']
python=3.8 -> libgcc-ng[version='>=7.3.0']

[idfarbanecha]

Hello @smajidian, I tried installing pbsim2 in a new environment with python 3.9 and did not encounter any issues.

Given that you have a conflict with libgcc-ng, try to add the conda-forge channel in your install command so that the solver has more options to resolve conflicts:

conda install -c bioconda -c conda-forge pbsim2

see this stack overflow question for reference