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genouest / biomaj2galaxy

BioMAJ post processes to manipulate Galaxy tool data tables
MIT License
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include datasetid #6

Closed nagoue closed 3 years ago

nagoue commented 3 years ago

Galaxy 19.09 Biomaj 3.10 Biomaj2galaxy 2.1.0

The data manager manual is mixing up dataset id and job id probably due to galaxy code evolution ? It is (now) required here to assigned separetely dataset id and job id otherwise this raised an error were Galaxy is looking for a job_id that refers to a dataset_id

abretaud commented 3 years ago

Cool, thanks @nagoue! The tests are failing for now due to something fixed in #5, I'll have a look at all this

abretaud commented 3 years ago

Arg. Forgot a quote there https://github.com/mesocentre-clermont-auvergne/biomaj2galaxy/pull/1/files#diff-6ac3f79fc25d95cd1e3d51da53a4b21b939437392578a35ae8cd6d5366ca5485R32 Can you add it (or grant me write perm on your branch)?

abretaud commented 3 years ago

Ok, now flake8 is complaining, could you make these changes (from #5) on your branch? https://github.com/genouest/biomaj2galaxy/pull/5/commits/0686e4a009cccaad3f0db8d7fdf769282b8b1e7d https://github.com/genouest/biomaj2galaxy/pull/5/commits/3bfed6a0236d099fb47c217643bdee910c183b0a https://github.com/genouest/biomaj2galaxy/pull/5/commits/f412d37c7a7bf10b3f378fae793983b3d66e34fb

abretaud commented 3 years ago

For this PR, could you update the name of the STAR data table everywhere in the code (or grant me access to your branch to do it)? It changed from rnastar_index2_versioned to rnastar_index2x_versioned in the latest version of the data manager

There's also a failure on a bowtie2 test, I don't know why... maybe it will go away by fixing rna star, who knows?

abretaud commented 3 years ago

Travis is horribly slow, but tests are passing now, I'm merging it now, and will switch to github actions on the master branch Merci beaucoup @nagoue !