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Use Snakemake tmpdir resource #319

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holtgrewe opened this issue Jan 5, 2023 · 0 comments · Fixed by #320
Closed

Use Snakemake tmpdir resource #319

holtgrewe opened this issue Jan 5, 2023 · 0 comments · Fixed by #320

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@holtgrewe
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Is your feature request related to a problem? Please describe.
A while ago, Snakemake introduced the tmpdir resource. We currently override tmpdir in the job script. This is bad.

Describe the solution you'd like
Implement a get_tmpdir() in the BaseStep class and implement the resource tmpdir in ResourceUsage. The behaviour should be as follows:

First, prefer to use ResourceUsage.tmpdir if set.

Then, fall back to:

  1. Configuration global_settings/tmpdir and interpret environment variables such as $HOSTNAME and $HOME. Introduce date +%Y%m%d as $TODAY.
  2. If not set, return environment variable $TMPDIR
  3. If not set, return tempdir.gettmpdir() as Snakemake does.

Describe alternatives you've considered
N/A

Additional context
N/A
holtgrewe added a commit that referenced this issue Jan 5, 2023
@holtgrewe
feat!: use snakemake tmpdir resource (#319)
336b48d 
You can use the following config snippet (top level key "global_config"):

    global_config:
      tmpdir: /data/wekafs-1/groups/cubi/scratch/holtgrem_c/$HOSTNAME/$TODAY
@holtgrewe holtgrewe linked a pull request Jan 5, 2023 that will close this issue
feat!: use snakemake tmpdir resource (#319) #320
Merged
holtgrewe added a commit that referenced this issue Jan 5, 2023
@holtgrewe
feat!: use snakemake tmpdir resource (#319) (#320)
c8512b0 
You can use the following config snippet (top level key "global_config"):

    global_config:
      tmpdir: /data/wekafs-1/groups/cubi/scratch/holtgrem_c/$HOSTNAME/$TODAY
@github-actions github-actions bot mentioned this issue Jan 5, 2023
Closed
@tedil tedil mentioned this issue Jun 28, 2024
Merged
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feat!: use snakemake tmpdir resource (#319) bihealth/snappy-pipeline
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@holtgrewe