Details
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Type:
Task
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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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:2
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Epic Link:
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Sprint:Spring 1, Spring 2
Description
Situation: Galaxy supports multiple file types for visualization in IGB. However, it is missing GFF and VCF file formats.
Task: Enable IGB to open Galaxy VCF and GFF format data sets
Instructions for running Galaxy locally: https://galaxyproject.org/admin/get-galaxy/
Attachments
Issue Links
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- Closed
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Activity
I've made a Galaxy help post to address this issue: https://help.galaxyproject.org/t/issue-upgrading-database-for-local-galaxy/17296
Since working on a similar ticket to enable Galaxy to display CRAM files in IGB, Galaxy has had several new releases come out. This has come with changes to the files they host for setting up local Galaxy instances and I am now having trouble running Galaxy locally.
When running sh run.sh to start the server, I get the following error:
galaxy.model.migrations.exceptions.OutdatedDatabaseError: Your galaxy database has version 3af58c192752, but this code expects version 312602e3191d. To upgrade your database, run `manage_db.sh upgrade`. For more options (e.g. upgrading/downgrading to a specific version) see instructions in that file. Please remember to backup your database before migrating.
Per that error, I then run ./manage_db.sh upgrade to upgrade my galaxy database. However, my database does not appear to be upgrading to the version specified by the previous error:
INFO:alembic.runtime.migration:Running upgrade 3af58c192752 -> c0959ad462b2, Add tool_id and tool_version to tool_landing_request table
This does appear to be a known issue per the instructions here: https://galaxyproject.org/admin/get-galaxy/#keep-your-code-up-to-date. However, the instructions for fixing this issue are minimal, so I'm stuck troubleshooting this issue for now.
While we wait, Dr. Freese and I tested these VCF and GFF updates by running a previous version of Galaxy locally. I am able to export VCF files from Galaxy to view in IGB, so that appears to be working. However, I cannot test GFF files effectively because there have been some codebase changes related to GFF files that Galaxy made between this old version and the new version I'm still unable to run. Further testing will need to be done once we hear back from the Help team.