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Add Snakemake workflow profile as override of local profile #268

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timtroendle opened this issue Jun 23, 2023 · 2 comments · Fixed by #361
Closed

Add Snakemake workflow profile as override of local profile #268

timtroendle opened this issue Jun 23, 2023 · 2 comments · Fixed by #361
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enhancement New feature or request good first issue Good for newcomers workflow Related to the design and execution of the workflow.

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@timtroendle
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What can be improved?

Snakemake 7.29.0 added the option to have a workflow profile that overrides local profiles. By default, this is profiles/default. We should use this mechanism to allow for local profiles.

As the workflow profile default works for us out of the box, we only need to update to 7.29.0. We can remove the env variable in the default environment.

Version

1.2.0.dev
@timtroendle timtroendle added enhancement New feature or request workflow Related to the design and execution of the workflow. labels Jun 23, 2023
@timtroendle timtroendle added the good first issue Good for newcomers label Feb 23, 2024
@timtroendle
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We should remove the cores parameter from the new workflow-profile, as this clearly is a per-machine, not a per-workflow restriction.

@timtroendle
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timtroendle commented Apr 15, 2024 •
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I tried this just now and there are caveats:

  • Not providing cores may not be a good idea, as Snakemake has no default value and will fail when no user config is provided.
  • The user/local profile is not activated automatically (in contrast to the default workflow profile) and its use is therefore not very user-friendly.

timtroendle added a commit to timtroendle/euro-calliope that referenced this issue Apr 15, 2024
@timtroendle
Update default profile to be a workflow-profile
8e8709a 
Default profile (in ``profiles/default`) is now the default workflow profile. Snakemake activates it automatically using the name. This allows the user to inject other profile parameters using the `--profile` cli option. This also allows us to provide the conda configuration as an addition to, rather than a replacement of, the default profile.

Fixes calliope-project#268
timtroendle added a commit to timtroendle/euro-calliope that referenced this issue Apr 15, 2024
@timtroendle
Update default profile to be a workflow-profile
2dc0987 
Default profile (in `profiles/default`) is now the default workflow profile. Snakemake activates it automatically using the name. This allows the user to inject other profile parameters using the `--profile` cli option. This also allows us to provide the conda configuration as an addition to, rather than a replacement of, the default profile.

Fixes calliope-project#268
timtroendle added a commit to timtroendle/euro-calliope that referenced this issue Apr 15, 2024
@timtroendle
Update default profile to be a workflow-profile
e2d0472 
Default profile (in `profiles/default`) is now the default workflow profile. Snakemake activates it automatically using the name. This allows the user to inject other profile parameters using the `--profile` cli option. This also allows us to provide the conda configuration as an addition to, rather than a replacement of, the default profile.

Fixes calliope-project#268
@timtroendle timtroendle mentioned this issue Apr 15, 2024
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enhancement New feature or request good first issue Good for newcomers workflow Related to the design and execution of the workflow.
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Update default profile to be a workflow-profile timtroendle/euro-calliope
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@timtroendle