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workDir and jobStore now default to (shared) tmp-outdir-prefix #5154

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gmloose
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@gmloose gmloose commented Nov 12, 2024

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gmloose commented Nov 12, 2024

Implements #5143.

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The code changes look good but I think as is this makes the documentation confusing for the non-CWL case.

Comment on lines 92 to 93
the workflow logs. Default is determined by the
variables (TMPDIR, TEMP, TMP) via mkdtemp. This
the workflow logs. Default is the temporary output
directory (see ``--tmp-outdir-prefix``). This
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There's only a notion of --tmp-outdir-prefix in the CWL runner; Python workflows an the WDL runner don't have it, and this documentation is meant to cover all three. So this probably needs to say that for CWL workflows the default --workDir comes from --tmp-outdir-prefix, but for other cases it still comes from mkdtemp.

Also, the help that Toil actually prints is here, and it also has the material about mkdtemp, so if in CWL mode that doesn't apply, we might want to change that text too. There we have access to a boolean cwl flag, so we could describe the CWL-related behavior when it is set and the non-CWL behavior otherwise.

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I reverted the change to the original text, and added a line about CWL workflows and --tmp-outdir-prefix. I don't know if you want it to be more elaborate.

I didn't touch the help that Toil prints. It was not completely clear to me where these changes had to be made, taking the cwl boolean into account.

This commit makes the following changes to the behaviour of the given command-line options:
* `tmp-outdir-prefix` defaults to `tmpdir-prefix`, unless given on the command-line
* `workDir` defaults to `tmp-outdir-prefix`, unless given on the command-line
* `jobStore` defaults to `tmp-outdir-prefix`, unless given on the command-line
* `coordinationDir` defaults to the default tmpdir-prefix, ignoring `tmpdir-prefix` when given on the command-line (rationale: this is a book-keeping location, that must be on a local 100% posix-compliant file system, because it uses file locks).
Updated the CLI documention for the `--workDir` option.
The jobstore cannot be put inside the working directory, because it may need to be retained (e.g. when --stats is set).
It now gets its own (temporary) directory, if not specified with the --jobstore option.
We do not need to create a working directory on the head node. We only need to create our jobstore here.
There's no need to set `options.tmp_outdir_prefix` here. It is not done in the current `master` branch either.
Improved the documentation of the `--workDir` option, by adding an explanation that the `--tmp-outdir-prefix` will be used for CWL workflows.
@mr-c mr-c force-pushed the issues/5143-workdir-and-jobstore-in-tmp-outdir-prefix branch from ec7b5ca to f71ddf3 Compare November 14, 2024 15:05
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@stxue1 is going to fix up the help here and merge this in.

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stxue1 commented Nov 20, 2024

@stxue1 stxue1 enabled auto-merge (squash) November 25, 2024 23:35
@stxue1 stxue1 disabled auto-merge November 26, 2024 22:27
@DailyDreaming DailyDreaming merged commit 89d8e53 into DataBiosphere:master Dec 2, 2024
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workDir and jobStore should default to (shared) tmp-outdir-prefix
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