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Automated pinned environments for snakemake #53
Description
Is your feature request related to a problem? Please describe.
Pinning environments in Snakemake is annoying since pixi's naming convention does not mach snakemake's.
We could automate this through tasks.
Describe the solution you'd like
[tasks.export-conda-spec]
description = "Export one Pixi environment/platform as a conda explicit spec"
args = ["env", "platform"]
cmd = "pixi workspace export conda-explicit-spec --environment '{{ env }}' --platform '{{ platform }}' workflow/envs/"
[tasks.rename-conda-spec]
description = "Rename one Pixi conda explicit spec to a Snakemake pin file"
args = ["env", "platform"]
cmd = "mv workflow/envs/{{ env }}_{{ platform }}_conda_spec.txt workflow/envs/{{ env }}.{{ platform }}.pin.txt"
[tasks.export-snakemake-pin]
description = "Export one Pixi environment/platform as a Snakemake-compatible conda pin file"
args = ["env", "platform"]
depends-on = [
{ task = "export-conda-spec", args = ["{{ env }}", "{{ platform }}"] },
{ task = "rename-conda-spec", args = ["{{ env }}", "{{ platform }}"] },
]
[tasks.export-snakemake-env]
description = "Export one Pixi environment as a conda environment YAML"
args = ["env"]
depends-on = [
{ task = "export-snakemake-pin", args = ["{{ env }}", "win-64"] },
{ task = "export-snakemake-pin", args = ["{{ env }}", "linux-64"] },
{ task = "export-snakemake-pin", args = ["{{ env }}", "osx-arm64"] },
]
cmd = "pixi workspace export conda-environment --environment '{{ env }}' workflow/envs/{{ env }}.yaml"Describe alternatives you've considered
Waiting until snakemake finally implements pixi?
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