Opened 10 months ago

Closed 8 months ago

#1028 closed enhancement (fixed)

Add support for StringTie data

Reported by: nicklas Owned by:
Priority: major Milestone: Relax v1.2
Component: net.sf.basedb.relax Keywords:
Cc:

Description (last modified by nicklas)

The relax server is currently only supporting "cufflinks" raw bioassays. We need to define the "stringtie" type in the same way as we do on the production server.

Once the raw data type has been defined, the release importer should probably work without (or with only minor) modifications.

The level 3 exporter plug-in currently has a section for handling Cufflinks and FPKM files. This need to the modified to support StringTie as well (and whatever file(s) we decide publish).

Change History (6)

comment:1 Changed 10 months ago by nicklas

  • Description modified (diff)

comment:2 Changed 8 months ago by nicklas

(In [4735]) References #1028: Add support for StringTie? data

The Relax installation wizard now creates the StringTie platform as a variant of the Sequencing platform. File types should automatically be linked when importing data from a StringTie release.

comment:3 Changed 8 months ago by nicklas

(In [4737]) References #1028: Add support for StringTie? data

The Level 3 exporter plug-in has been updated to also handle INCA2 annotation types.

It will also export the "Generic raw data" file in the StringTie case (this should be the "gene.tsv" file).

comment:4 Changed 8 months ago by nicklas

(In [4769]) References #1028: Add support for StringTie? data

The Cohort exporter has been redesigned to allow raw bioassay lists with multiple raw data types. The generic file name "rawbioassay.txt" is now always used for raw bioassays. This file also inlcudes an extra column: "RawBioAssay? type".

This change breaks the Level3 export so that it doesn't export any files.

comment:5 Changed 8 months ago by nicklas

(In [4771]) References #1028: Add support for StringTie? data

The Level 3 export should now be able export lists with more than one type of raw data. It should be able to automatically select the correct information and files depending on the raw data type (for cufflinks and stringtie).

comment:6 Changed 8 months ago by nicklas

  • Resolution set to fixed
  • Status changed from new to closed

Seems to work after full test of releasing data from reggie via relax to a level 3 server.

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