Issue
I've been failing to install sea-snap mainly because conda was giving me issues. I tried step-by-step removing packages and got nowhere. Now I figured out that simply using a yaml file to create an env somehow makes my conda install a very old snakemake version (which won't work):
This works (snakemake ends up with the current 7.18)
mamba create -n seasnap-test --dry-run snakemake bamtools bedtools salmon samtools star
This, however, does not (snakemake is set to 4.0.0):
mamba env create -f test.yaml -n seasnap-test --dry-run
Issue I've been failing to install sea-snap mainly because conda was giving me issues. I tried step-by-step removing packages and got nowhere. Now I figured out that simply using a yaml file to create an env somehow makes my conda install a very old snakemake version (which won't work):
This works (snakemake ends up with the current 7.18)
mamba create -n seasnap-test --dry-run snakemake bamtools bedtools salmon samtools star
This, however, does not (snakemake is set to 4.0.0):
mamba env create -f test.yaml -n seasnap-test --dry-run
Possible solution The channel priority looks off,
conda-forge
should come first inconda_env.yaml
.Additional info Similar issue with solution: https://github.com/bioconda/bioconda-recipes/issues/34190