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Run galaxy with default tools included#1381

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bernt-matthias wants to merge 2 commits intogalaxyproject:masterfrom
bernt-matthias:topic/serve-with-default-tools
Closed

Run galaxy with default tools included#1381
bernt-matthias wants to merge 2 commits intogalaxyproject:masterfrom
bernt-matthias:topic/serve-with-default-tools

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@bernt-matthias
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I wanted to test some Galaxy tools and needed the collection operations. So I thought it might be a good idea to serve planemo with Galaxy's default tools installed:

Screenshot from 2023-08-04 15-59-25

Not sure what happens if some one calls planemo test/serve on one of the builtin tools....

Alternatively one could use --extra_tools but then the tools are just installed flat in the tool menu.

bernt-matthias added a commit to bernt-matthias/planemo that referenced this pull request Aug 4, 2023
linter complained about this over here galaxyproject#1381
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
@mvdbeek
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mvdbeek commented Aug 7, 2023

Can you expose a --tool_conf argument instead (and check that --shed_tool_conf doesn't do the job already) ?

@bernt-matthias
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Can you expose a --tool_conf argument instead?

Could be done I guess. But it would be inconvenient for users who so not have a clone of Galaxy.

@mvdbeek
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mvdbeek commented Aug 7, 2023

Fine, but then at least make this optional ?

@jmchilton
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Could we have --extra_tools be able to take toolbox conf in addition to actual tools and directory. Also I guess we use the name stock tools in the workflow docs for planemo - so maybe add like a flag --include_stock_tools that is short-hand for enabling the behavior here (--extra_tools with a the tool conf sample as the target).

@bernt-matthias
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Can you expose a --tool_conf argument instead (and check that --shed_tool_conf doesn't do the job already) ?

Seems that --shed_tool_conf already does the trick (at least with --galaxy_root and using the sample tool conf from this directory).

@bernt-matthias bernt-matthias deleted the topic/serve-with-default-tools branch January 14, 2024 16:25
@kostrykin
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kostrykin commented Mar 3, 2026

How exactly do I get the correct parameter to pass to --shed_tool_conf when running planemo serve?

(I have no local Galaxy, if this matters)

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5 participants