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:2
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Epic Link:
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Sprint:Spring 6, Summer 4
Description
Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.
Task: Update the IGB synonyms.txt with any missing Galaxy synonyms. See IGBF-1879 for additional details.
Galaxy genome API: https://usegalaxy.org/api/genomes
Galaxy Europe genome API: https://usegalaxy.eu/api/genomes
UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1880 [ 17970 ] |
| Description |
Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.
Task: Update the IGB synonyms.txt with any missing Galaxy synonyms. Galaxy genome API: https://usegalaxy.org/api/genomes Galaxy Europe genome API: https://usegalaxy.eu/api/genomes UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes |
Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.
Task: Update the IGB synonyms.txt with any missing Galaxy synonyms. See Galaxy genome API: https://usegalaxy.org/api/genomes Galaxy Europe genome API: https://usegalaxy.eu/api/genomes UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes |
| Assignee | Paige Kulzer [ pkulzer ] |
| Sprint | Spring 3 [ 212 ] | Spring 4 [ 213 ] |
| Sprint | Spring 4 [ 213 ] |
| Rank | Ranked higher |
| Sprint | Spring 6 [ 215 ] |
| Rank | Ranked lower |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
- This opened a custom genome in IGB.
- This opened the correct genome in IGB.
- Below is a table summarizing the genomes that we're including in synonyms.txt without the correct Galaxy key:
| Genome | Galaxy Key |
| A_thaliana_Jan_2004 | araTha1*** |
| A_thaliana_Apr_2008 | arabidopsis_tair8 |
| A_thaliana_Jun_2009 | arabidopsis |
| H_exemplaris_Z151_Apr_2017 | H_exemplaris_Z151 |
| Y_lipolytica_CLIB122_Jul_2004 | GCF_000002525.2 |
***This key (araTha1) is already listed in synonyms.txt with a different genome. Galaxy correlates araTha1 with TAIR7, we've correlated it with TAIR9/TAIR10, and UCSC correlates it with TAIR10. Which is correct? Update: I believe TAIR10 is correct
Please see attached for a copy of the spreadsheet I compiled listing the genomes hosted by Galaxy/Galaxy EU as well as the genomes hosted by UCSC and IGB.
Ready for review!
| Attachment | galaxy-genomes-to-add-to-synonyms.csv [ 18667 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
| Attachment | UniqueGalaxyGenomes.html [ 18668 ] | |
| Attachment | UniqueGalaxyGenomes.R [ 18669 ] |
| Sprint | Spring 6 [ 215 ] | Spring 6, Spring 7 [ 215, 216 ] |
| Rank | Ranked higher |
| Genome | Galaxy Key | |
| A_thaliana_Jan_2004 | araTha1*** |
|
| A_thaliana_Apr_2008 | arabidopsis_tair8 |
|
| A_thaliana_Jun_2009 | arabidopsis |
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| H_exemplaris_Z151_Apr_2017 | H_exemplaris_Z151 |
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| Y_lipolytica_CLIB122_Jul_2004 | GCF_000002525.2 |
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Paige Kulzer - I marked some above as needing to be double checked, otherwise please go ahead and add the Galaxy key values to the synonyms.txt file in the SVN repository.
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 6, Spring 7 [ 215, 216 ] | Spring 6, Summer 1 [ 215, 218 ] |
| Sprint | Spring 6, Summer 1 [ 215, 218 ] | Spring 6, Summer 3 [ 215, 220 ] |
| Sprint | Spring 6, Summer 3 [ 215, 220 ] | Spring 6, Summer 4 [ 215, 221 ] |
| Genome | Galaxy Key |
| A_thaliana_Apr_2008 | arabidopsis_tair8 |
| A_thaliana_Jun_2009 | arabidopsis |
| Y_lipolytica_CLIB122_Jul_2004 | GCF_000002525.2 |
This is the final table with the changes that need to be made to IGB's synonyms.txt. Rather than making these changes via SVN, they will be made to IGB's version of synonyms.txt. That task has been captured by a ticket Dr. Freese just made (IGBF-4266) so I will now close this ticket and work on that one.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
First steps: