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
I've created a file called "cram.xml" by copying "bam.xml", replacing every instance of "bam" with "cram" in that copied file, then saving it as "cram.xml".
Before I submit a PR to the Galaxy project, I want to test that this file is working locally. To do this, I've set up a Galaxy instance on my computer by following the instructions I found here: https://galaxyproject.org/admin/get-galaxy/
I've added a test cram file and a test bam file to my Galaxy History. Clicking the Visualize icon on the bam file brings up the usual display in IGB option, but there are still no display options available for the cram file.
I found a tutorial called "Displaying Datasets at External Display Applications / Websites using GEDAs" which walks through the process of enabling Galaxy to send files to genome browsers for visualization - https://galaxyproject.org/admin/tools/external-display-applications-tutorial/.
The tutorial indicates that the next step after creating a new XML definition file is to edit datatypes_conf.xml with the location of the new XML file. However, I am currently unable to locate that file.
I've located datatypes_conf.xml and have added the following line of code to it:
<display file="igb/cram.xml"/>
Unfortunately, I'm still not able to see the display in IGB option for the cram file in my local Galaxy instance.
I've tracked down a paper that Galaxy published on this topic, here's a link: https://pmc.ncbi.nlm.nih.gov/articles/PMC8845068/#SD1
The steps for adding an external display application appear to be the same in the paper as they are in the tutorial.
I've figured out the issue - I simply needed to push my commit and restart my local Galaxy instance in order to see my changes reflected.
Commit: https://github.com/galaxyproject/galaxy/commit/63065138524226de8e4da93c701a91d77815fbc5
For testing:
1. Clone the Galaxy repo to your computer
git clone https://github.com/galaxyproject/galaxy.git
2. Start the Galaxy server (this may take a couple minutes)
sh run.sh
3. Access the Galaxy server from a web browser at the following link: http://localhost:8080/
4. Add a CRAM file to your Galaxy History (sample data from another ticket can be found here: https://drive.google.com/drive/folders/1bbw3eqvmjUvgYfWqv7Wmkl-o9SlQUeFM?usp=sharing)
5. Click the Visualize (bar chart) icon.
6. Observe that the display in IGB option is now present.
7. Click View next to display in IGB.
8. Switch to an IGB window and observe that the CRAM file has been added to IGB.
9. Zoom to the following coordinates: Chr1:6,550-8,753
10. Click Load Data.
11. Observe that data has been loaded on the CRAM file track.
Different testing instructions are also available in the comments of one of the linked tickets (IGBF-2160).
Fetched Paige's branch with cram support:
git fetch https://github.com/paige-kulzer/galaxy.git cram-support:cram-support
git checkout cram-support
Note: There is a weird error that will appear if the absolute path to your Galaxy repository on your local computer is too long. This prevented me from running Galaxy locally. The only fix I could find was to put my local Galaxy repository closer to root so that the absolute path wasn't as long.
Was able to run Galaxy locally and see Paige's changes after uploading a CRAM file. I was able to view the CRAM file stored in my local Galaxy in IGB. Interestingly, IGV does not appear as an option for viewing a CRAM file (this is also true on the current released version of Galaxy, I checked).
Commit looks good.
Paige Kulzer - ready for pull request
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