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: 10.2.0
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Labels:None
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Story Points:0.25
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Epic Link:
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Sprint:Winter 1, Spring 1, Spring 2, Spring 3
Description
Situation: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.
Task: Add the following to IGB's species.txt and synonyms.txt files:
species.txt
Aedes albopictus Asian tiger mosquito A_albopictus Capitella teleta Capitella teleta C_teleta Dama dama Fallow deer D_dama Hydra vulgaris Swiftwater hydra H_vulgaris Oryzias latipes Japanese medaka O_latipes Vanessa cardui Painted lady V_cardui
synonyms.txt
A_albopictus_Jan_2024 AalbF5 C_teleta_Jan_2013 Capca1 D_dama_Nov_2023 ASM3311817v1 H_vulgaris_Feb_2022 HydraT2T_AEP O_latipes_Jul_2017 ASM223467v1 V_cardui_Feb_2021 ilVanCard2.1
Attachments
Activity
dama dama
Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/3374785b8199efff271b80abc20edfdbfff58fce
To test using my branch:
- Build and run IGB
- Check each of the above mentioned genomes such that the species and synonyms appear correctly.
Cloned and fetched Nowlan's branch for testing on Mac, here's what I found:
- Aedes albopictus - OK
- Capitella teleta - OK
- Dama dama - OK
- Hydra vulgaris - You've listed "Fresh-water polyp" as an alternative name for this species in the Description of this ticket, but in IGB I'm seeing "Swiftwater hydra". Which is correct?
- Oryzias latipes - The two O_latipes subspecies have "Japanese medaka" as their alternative name. For consistency, maybe we should update "Medaka" to "Japanese medaka" for this species.
- Vanessa cardui - OK
Moving this back to do, please review the notes I've left here and make changes accordingly.
Updated branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4006
Tested again on Mac, my notes for the Hydra vulgaris and Oryzias latipes genomes have been addressed. I'm now seeing the correct species and genome names for each of the six species. Ready for PR!
PR is merged, new installers are built and deployed to early access section on bioviz.org.
Ready for testing.
Downloaded the early access version of IGB from BioViz.org and tested on Mac. All species and synonyms are displaying when hovering over these genomes in the Species and Genome Version drop-down menus. Reference sequences loaded when I zoomed into a location on each of these genomes and clicked Load Sequence. No errors in the Log.
Closing this ticket!
Need to update the species.txt for O latipes:
Oryzias latipes Japanese rice fish (Medaka) O_latipes oryLat Oryzias_latipes oryzias_latipes