Entering edit mode
2.3 years ago
tsogurlu
•
0
Hello everyone,
I am new into this creating environment thing and not an expert in bioinformatics. So I do not know maybe this is a dumb question. I try to install packages, however I encountered with this warning message:
Command:
mamba env create --quiet --file "/cta/users/tsogurlu/2023/pipeline/.snakemake/conda/9b5c4f48c50437d93c14f2f0fe0ccc67.yaml" --prefix "/cta/users/tsogurlu/2023/pipeline/.snakemake/conda/9b5c4f48c50437d93c14f2f0fe0ccc67"
Output:
Encountered problems while solving:
- nothing provides libzlib >=1.2.11,<1.3.0a0 needed by samtools-1.15-h1170115_1
However when I have checked the libzlib (whatever it is) by:
conda list | grep libzlib
I got:
libzlib 1.2.13 hd590300_5 conda-forge
So what is the problem ? The version is already bigger than libzlib >=1.2.11. Did I misunderstand the warning message ?
Many thanks
Did you specified your channels in the install command? (e.g.
mamba install -c conda-forge -c bioconda samtools=1.15 ....) Could you share your install command?OP do this, very good chance your problem is the lack of
conda-forgechannelHi, Since this is a pipeline, I do not know. I have searched for the installing command. While searching, I realized that the problem is, I guess, is related to creating environment rather than installing.
you should have, somewhere in your snakemake project an environment file (in yaml or json format). Check if conda-forge is in a specified channel in this file
current samtools is 1.19, why do you need 1.15 ? https://github.com/samtools/samtools/releases/
To tell the truth, I am using a new pipeline. The creators chose to install this version. I've just tried to run it. Maybe I can give this feedback to them. Do you have any idea about my problem ? I would really appreciate any suggestion.