Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Winter 1, Spring 1, Summer 4
Description
Situation: We've added support for the CRAM file format in IGB and are now updating our documentation to include this new file format. In order to update our Galaxy release documentation (https://wiki.bioviz.org/confluence/display/ITD/Galaxy), we need to enable Galaxy to create "display in IGB" links for CRAM files.
Task:
- Clone the Galaxy repo and deploy it on a local machine for development and testing.
- Create and add a new file, "cram.xml", to Galaxy's source code (link: https://github.com/galaxyproject/galaxy/tree/1b11742252b6cfe6b6cc1ee4c52f7f4ffa386f06/lib/galaxy/datatypes/display_applications/configs/igb). This may be as simple as copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml".
- Submit a pull request with that new file to the latest Galaxy release branch.
- Determine how to test that the new capability is working as expected.
- Once finished with testing, next steps will be to make a new ticket for adding a CRAM file to the "Open Galaxy Files in Integrated Genome Browser" History (https://usegalaxy.org/published/history?id=4d6cb5a8a3640b22). I'd suggest maybe using the one that was subsetted to a smaller size as part of
IGBF-3841.
Attachments
Issue Links
Activity
Here's a link to the documentation for creating Galaxy Tool XML Files: https://docs.galaxyproject.org/en/latest/dev/schema.html
Tested on:
Galaxy EU (link) - loaded correctly in IGB (data on hg38 on chromosome 2)
Galaxy US (link) - loaded correctly in IGB (data on hg38 on chromosome 2)
Closing ticket.