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: 9.0.2 Minor Release
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Labels:
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Story Points:0.25
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Sprint:Fall 2018 Sprint 3
Description
Modify species.txt in IGB codebase
Add line from:
http://igbquickload.org/quickload/species.txt
Preserve alphabetical order in file.
Attachments
Issue Links
Activity
| Workflow | Fall 2019 Workflow Update [ 19955 ] | Revised Fall 2019 Workflow Update [ 22076 ] |
| Workflow | Loraine Lab Workflow [ 18129 ] | Fall 2019 Workflow Update [ 19955 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Resolution | Done [ 10000 ] | |
| Status | Needs Testing [ 10002 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
Passes functional review.
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Ready for Pull Request [ 10304 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
Fixed on branch https://bitbucket.org/aloraine/alorainefork/branch/IGBF-1423
To test:
- Reset preferences to defaults
- De-activate main IGB Quickload (which contains species.txt file listing potato; IGB uses species.txt files from Quickload sites in addition to its own personal species.txt file packaged with the installer)
- Add this test Quickload site: http://lorainelab-quickload.scidas.org/IGBF-1423
- Quit then re-start IGB
- Check that the species and genome menus list the potato genome, with tooltip on mouse-over the species menu entry
Note: To re-create this site in current working directory:
- svn co https://svn.bioviz.org/repos/genomes/quickload/S_tuberosum_DM_Jul_2011
- wget -O - http://igbquickload.org/quickload/contents.txt | grep S_tuberosum_DM_Jul_2011 > contents.txt
svn (subversion) lets you check out part of a repository. This is the potato genome directory.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Summary | Add potato genome assembly synonyms to IGB species.txt and synonyms.txt | Add potato genome assembly synonyms to IGB species.txt |
| Comment |
[ Correction:
*Only* modify species.txt Add line from: http://igbquickload.org/quickload/species.txt Preserve alphabetical order in file. Also, note we are now supporting the July 2011 version 4.03 release and not the version 4.04 Jan 2016 release. ] |
| Labels | Beginner | Intermediate |
| Description |
Add (or check to see if it is already there) the 4.03 DM potato genome to IGB synonyms.txt and species.txt files.
To my knowledge, no other genome browser system is supporting this assembly, so there are no synonyms at the moment. For the name of the species, see the corresponding line in "contents.txt" in contents.txt genome assembly listing. See https://svn.bioviz.org/viewvc (Feel free to ask Dr. Loraine if you have questions.) |
Modify species.txt in IGB codebase
Add line from: http://igbquickload.org/quickload/species.txt Preserve alphabetical order in file. |
| Description |
Add (or check to see if it is already there) the 4.04 DM potato genome to IGB synonyms.txt and species.txt files.
IGB name for the assembly is: S_tuberosum_DM_Jan_2016 To my knowledge, no other genome browser system is supporting this assembly, so there are no synonyms at the moment. For the name of the species, see the corresponding line in "contents.txt" in contents.txt genome assembly listing. See https://svn.bioviz.org/viewvc (Feel free to ask Dr. Loraine if you have questions.) |
Add (or check to see if it is already there) the 4.03 DM potato genome to IGB synonyms.txt and species.txt files.
To my knowledge, no other genome browser system is supporting this assembly, so there are no synonyms at the moment. For the name of the species, see the corresponding line in "contents.txt" in contents.txt genome assembly listing. See https://svn.bioviz.org/viewvc (Feel free to ask Dr. Loraine if you have questions.) |
| Assignee | Ann Loraine [ aloraine ] |
Merged into upstream master (git@bitbucket.org:lorainelab/integrated-genome-browser.git)