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eggnog mapper: implement search and annotation phase as additional separate tools #676

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bernt-matthias
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@bernt-matthias bernt-matthias commented Jul 27, 2022

for rationale see README

TODO:

  • separate output options that apply only to annotation / search phase -> macros

@bgruening
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Having those 3 steps in one tool is not an option?

@bernt-matthias
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Having those 3 steps in one tool is not an option?

I do not see how to map the steps to different destinations if implemented in one tool (dynamic destinations might be an option, but many sites use static destinations.. Like mine ;))

@bernt-matthias
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Btw. Linting failures are due to the missing updates of the tool-util package for 21.01. Any idea how to get this on the way?

@bernt-matthias
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Having those 3 steps in one tool is not an option?

Let my just add #727 to this PR ..

@bernt-matthias
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Let my just add #727 to this PR ..

I reconsidered (because --dbmem was already handled here) and just left it as is. I'm happy to change to an entirely admin-controlled behavior, i.e. to use --dbmem only if the admin sets it as in #727

- more consistent macro names
- readme reformulation
@bgruening
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Ship it!

@bernt-matthias bernt-matthias merged commit 468bd31 into galaxyproteomics:master Sep 4, 2023
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@bernt-matthias bernt-matthias deleted the eggnog_separate branch September 4, 2023 12:23
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2 participants