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
PR has been submitted to the Galaxy codebase via GitHub: https://github.com/galaxyproject/galaxy/pull/19428
The PR has been merged - ready for review!
I'm not seeing a view option for a CRAM file in the current release of Galaxy. It looks like the PR has been merged, but they have not released the new version of Galaxy. For now will bump this ticket to a future sprint for testing.
As of today, Galaxy releases page reports that the latest release was Jan 25. The PR was merged in Feb. So, the new feature is not available on the latest release of Galaxy.
Moving this into the backlog.
Here's a link to the documentation for creating Galaxy Tool XML Files: https://docs.galaxyproject.org/en/latest/dev/schema.html