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Add python-chado tools #17

Merged
merged 4 commits into from
Jun 21, 2018
Merged

Add python-chado tools #17

merged 4 commits into from
Jun 21, 2018

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abretaud
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Some wrappers for python-chado, adapted from https://github.com/galaxy-genome-annotation/python-chado/tree/master/galaxy to make them a little prettier when possible
It's still WIP as some of them are broken, and I'd like to had more fancy stuff (like pg_tools some day??)

hexylena
hexylena previously approved these changes Jun 11, 2018
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Love the addition of the code file! This will make it way more user friendly.

@abretaud abretaud changed the title [WIP] Add python-chado tools Add python-chado tools Jun 20, 2018
@abretaud
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Ok, these tools should be ok now, it would be cool to have a quick review before merging it if you have time!
I'm not very proud of https://github.com/galaxy-genome-annotation/galaxy-tools/pull/17/files#diff-58b58b36cf628902782add4a9a13ae66R62, but I see no other way to make sure that a gff file is loaded before loading featureprops in a workflow for example...
I found a few bugs in python-chado, so I'll release the 2.1.2 version today.

@hexylena
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I've done exactly that hack before. I really wish galaxy would include some 'virtual' way of doing this without defining these files. I don't think there is a better option and that works well enough. Better than scheduling the job and just doing a while check-if-ok do; sleep 1; done; in the tool.

@abretaud
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It seems like I need a new review before merging this, @erasche would you have time for it? (it shouldn't break anything though, just new tools)

@abretaud
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thanks!

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2 participants