Ticket #23 (accepted defect)

Opened 3 years ago

Last modified 2 years ago

Update Galaxy with Excel upload support

Reported by: business@… Owned by: s.h.sikkema@…
Priority: major Milestone:
Component: Galaxy instance Version:
Keywords: Cc:

Description

Right now Excel does not understand Excel files when uploaded. Can we fix that?

 https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Excel_upload

 http://wiki.g2.bx.psu.edu/Admin/FAQ#Configuring_Galaxy_so_a_tool_can_properly_generate_an_Excel_file

Siemen suggested creating a tool that converts Excel to tabular. Any thoughts?

Change History

Changed 3 years ago by business@…

Leon suggested looking into the Galaxy public toolshed, but as far as I could see there's no Excel tool their either.

Changed 3 years ago by business@…

Changed 2 years ago by business@…

  • milestone set to 0.2.1

Changed 2 years ago by s.h.sikkema@…

  • status changed from new to accepted
  • owner set to s.h.sikkema@…

Changed 2 years ago by s.h.sikkema@…

Locally I have this working. I used the code from matrixImporter. Can be run using groovy or java on server (when compiled with groovyc). Problem is: Galaxy does not play nice with uploading of xls or xlsx files. Tried recreating uploader but to no avail... Workaround: zip files first and then upload -- galaxy unzips them -- and convert.

Changed 2 years ago by business@…

See discussion  http://galaxy-development-list-archive.2308389.n4.nabble.com/Excel-upload-problems-td4173225.html#a4174413

Next step is to try suggestion of Joe Cruz, and try if that works too for xlsx.

Changed 2 years ago by business@…

  • milestone 0.2.1 deleted

Changed 2 years ago by s.h.sikkema@…

Tried the solution and it works. But not for xlsx files. See discussion thread.

Changed 2 years ago by business@…

Suggestion: add the tool for XLS to the galaxytools nbic project?  https://trac.nbic.nl/galaxytools/

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