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:3
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Epic Link:
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Sprint:Spring 3, Spring 4, Spring 5
Description
Situation: We are hosting our subversion repository on our own EC2. The larger size of the repository is expensive.
Task: Remove the 2bit file from the svn repository for older "legacy" genome versions, such as older versions of the human or mouse genomes. Then use the annots.xml "name" attribute to point to that same file hosted on the UCSC Genome Web (link: https://hgdownload.soe.ucsc.edu/gbdb/) and set "reference" to true (see https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml for more details).
Attachments
Issue Links
- relates to
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IGBF-2537 Enable Quickload to specify the 2bit file for a genome
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2323 [ 18477 ] |
| Link | This issue relates to IGBF-4030 [ IGBF-4030 ] |
| Attachment | 2bit_sizes.txt [ 18646 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Description |
Situation: We are hosting our [subversion repository|https://svn.bioviz.org/viewvc/genomes/quickload/] on our own EC2. The larger size of the repository is expensive.
Task: Remove the 2bit file from the svn repository for older "legacy" genome versions, such as older versions of the human or mouse genomes. Then use the annots.xml "name" attribute to point to that same file hosted on the UCSC Genome Web (link: [https://hgdownload.soe.ucsc.edu/gbdb/|https://hgdownload.soe.ucsc.edu/gbdb/]) and set "index" to true (see [https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml|https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml] for more details). |
Situation: We are hosting our [subversion repository|https://svn.bioviz.org/viewvc/genomes/quickload/] on our own EC2. The larger size of the repository is expensive.
Task: Remove the 2bit file from the svn repository for older "legacy" genome versions, such as older versions of the human or mouse genomes. Then use the annots.xml "name" attribute to point to that same file hosted on the UCSC Genome Web (link: [https://hgdownload.soe.ucsc.edu/gbdb/|https://hgdownload.soe.ucsc.edu/gbdb/]) and set "reference" to true (see [https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml|https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml] for more details). |
| Sprint | Spring 4 [ 213 ] | Spring 3 [ 212 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | 2bit_sizes_3_7_2025.txt [ 18649 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Ann Loraine [ aloraine ] |
| 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 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Pranav Bhatia [ pbhatia1 ] |
| Sprint | Spring 3 [ 212 ] | Spring 3, Spring 4 [ 212, 213 ] |
| Rank | Ranked higher |
| Assignee | Pranav Bhatia [ pbhatia1 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Sprint | Spring 3, Spring 4 [ 212, 213 ] | Spring 3, Spring 4, Spring 5 [ 212, 213, 214 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Ann Loraine [ aloraine ] |
| 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 ] |