Conda environment creation fails due to package conflicts

[AlmogAngel]

Hello,

Firstly, thank you for the work that's been put into developing this pipeline.

I've encountered an issue following the instructions provided in the documentation. I used "XinY_4Decon" as the example input. After installation, I attempted to run the snakemake --use-conda —cores N command several times unsuccessfully.

The problem is with creating a conda environment due to numerous package conflicts. I have provided the log message below for more context:

Building DAG of jobs...
Creating conda environment Modules/MuSiC/env.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from CATD/Modules/MuSiC/env.yaml:
Command:
mamba env create --quiet --file "CATD/.snakemake/conda/b5933d7859c3c746082c318304027e7a_.yaml" --prefix "CATD/.snakemake/conda/b5933d7859c3c746082c318304027e7a_"
Output:
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
...
Could not solve for environment specs
The following packages are incompatible
...

The error message lists several packages, including 'c-ares', 'libdeflate', and many 'r-' packages such as 'r-brio', 'r-digest', etc., stating: <package name and version> is uninstallable because it conflicts with any installable versions previously reported;

Any help or suggestions be appreciated.

Almog

[annavpo]

Hi Almog,

Based on the errors, I think the problem comes from either conda or mamba. Could you please try to change the channel priorities to flexible or disabled?

conda config --set channel_priority disabled

https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html

Best,

Anna