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

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

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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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@adamnovak adamnovak linked an issue Nov 13, 2024 that may be closed by this pull request
workDir and jobStore should default to (shared) tmp-outdir-prefix #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.

docs/running/cliOptions.rst Outdated
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.

@gmloose @mr-c
Let workDir and jobStore default to tmp-outdir-prefix
38b0a8c 
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).
@gmloose @mr-c
Update documentation
bb79ec1 
Updated the CLI documention for the `--workDir` option.
@gmloose @mr-c
Jobstore needs its own directory
5850f49 
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.
@gmloose @mr-c
Do not create working directory on head node
c7b003e 
We do not need to create a working directory on the head node. We only need to create our jobstore here.
@gmloose @mr-c
No need to set options.tmp_outdir_prefix
a373ff1 
There's no need to set `options.tmp_outdir_prefix` here. It is not done in the current `master` branch either.
@gmloose @mr-c
Improve documentation of workDir option
f71ddf3 
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

Testing the equivalent over at https://github.com/DataBiosphere/toil/tree/issues/5143-workdir-and-jobstore-in-tmp-outdir-prefix

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@stxue1 stxue1 stxue1 approved these changes

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workDir and jobStore should default to (shared) tmp-outdir-prefix
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