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Fail to install - channel priority issue #20

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eudesbarbosa opened this issue Nov 29, 2022 · 1 comment
Open

Fail to install - channel priority issue #20

eudesbarbosa opened this issue Nov 29, 2022 · 1 comment

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@eudesbarbosa
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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

$ cat test.yaml

channels:
- bioconda
- conda-forge
- defaults
dependencies:
- snakemake
- samtools
- bedtools
- bamtools
- salmon
- star

Possible solution
The channel priority looks off, conda-forge should come first in conda_env.yaml.

Additional info
Similar issue with solution: bioconda/bioconda-recipes#34190

@eudesbarbosa
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CC @Nicolai-vKuegelgen

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