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Add datatype definition for AGP assemblies

Open davebx opened this issue 3 years ago • 8 comments

This adds support for the "A Golden Path" 2.0 assembly file format created by NCBI, as requested at the VGP meeting earlier this week.

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davebx avatar Oct 06 '21 16:10 davebx

It's tailing @davebx ... maybe a pure subclass datatype is enough. Do we expect many upload of that type that we need a sniffer?

bgruening avatar Oct 07 '21 20:10 bgruening

@bgruening I have a fix for the upload datatype test on my local branch, and I'm also almost done with a data provider for the datatype.

davebx avatar Oct 08 '21 09:10 davebx

Thanks for the feedback, @davelopez, this type annotation stuff is new to me.

davebx avatar Oct 12 '21 14:10 davebx

@davebx @mvdbeek would it be possible to get this into the next release. Usually that is ok for normal data types, this touches a little bit more.

bgruening avatar Oct 12 '21 18:10 bgruening

Is it already finished? @davebx

gallardoalba avatar Oct 21 '21 08:10 gallardoalba

Should we apply this to 21.09? Merge is dev and backport?

bgruening avatar Oct 21 '21 08:10 bgruening

@davebx can you get this into 21.09?

bgruening avatar Oct 23 '21 21:10 bgruening

We would need this for the Biohackathon. @davebx any change to get this fixed today?

bgruening avatar Nov 09 '21 11:11 bgruening

Seems that this is already in https://github.com/galaxyproject/galaxy/pull/12891

bernt-matthias avatar Jan 22 '23 14:01 bernt-matthias