Details
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Type:
Improvement
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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:
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Story Points:2
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Epic Link:
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Sprint:Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Spring 5 2021 May 17 - May 28
Description
This ticket was first worked on in 2014 and needs to be re-visited because Galaxy code base has progressed and many new genome versions are available.
The Galaxy software relies heavily on the UCSC Genome Browser informatics system to support many different genome versions. There's a "cron job" that Galaxy admin's periodically run to update genome version data in Galaxy. We need to understand how that works to make sure that IGB's synonyms system stays up to date with Galaxy.
The script(s) run during the cron job reside in:
The script in this directory that "kicks off" the update is updateucsc.sh.sample.
It also handles getting length files with chromosome names and sizes. Note that this script also manages import of non-ucsc genome names. Look at the script to see how that aspect is working.
The above is actually a legacy system but has been used for a long time and seems to work quite well. In addition, there's a "data manager" system that allows an admin to use the Galaxy UI to define new genomes.
Each genome version is identified by a "dbkey" that in the case of ucsc genomes, is identical to ucsc genome version names.
An example dbkey is "apiMel2", which is IGB, is called "A_mellifera_Jan_2005"
Dan Blankenberg (https://galaxyproject.org/people/dan/) notes that there may actually be a REST endpoint that can report the dbkeys for all genome versions supported in a given Galaxy instance. If not, he recommends we open a ticket in Galaxy github requesting this.
Galaxy also keeps track of a user-friendly name that is displayed to users. This is equivalent to column 2 in IGB Quickload's contents.txt file – see http://igbquickload.org/quickload/contents.txt.
For this task, check that the synonyms.txt file includes all genome versions supported by Galaxy. If not, update it.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | David Norris [ dcnorris ] |
| Story Points | 0.5 | |
| Sprint | Summer 2019 Sprint 11 [ 70 ] | |
| Labels | Intermediate |
| Description |
This ticket was first worked on in 2014 and needs to be re-visited because Galaxy code base has progressed and many new genome versions are available.
The Galaxy software relies heavily on the UCSC Genome Browser informatics system to support many different genome versions. There's a "cron job" that Galaxy admin's periodically run to update genome version data in Galaxy. We need to understand how that works to make sure that IGB's synonyms system stays up to date with Galaxy. The script(s) run during the cron job reside in: * https://github.com/galaxyproject/galaxy/tree/dev/cron The script in this directory that "kicks off" the update is updateucsc.sh.sample. It also handles getting length files with chromosome names and sizes. Note that this script also manages import of non-ucsc genome names. Look at the script to see how that aspect is working. The above is actually a legacy system but has been used for a long time and seems to work quite well. In addition, there's a "data manager" system that allows an admin to use the Galaxy UI to define new genomes. Each genome version is identified by a "dbkey" that in the case of ucsc genomes, is identical to ucsc genome version names. An example dbkey is "apiMel2", which is IGB, is called "A_mellifera_Jan_2005" Dan Blankenberg (https://galaxyproject.org/people/dan/) notes that there may actually be a REST endpoint that can report the dbkeys for all genome versions supported in a given Galaxy instance. If not, he recommends we open a ticket in Galaxy github requesting this. Galaxy also keeps track of a user-friendly name that is displayed to users. This is equivalent to column 2 in IGB Quickload's contents.txt file -- see http://igbquickload.org/quickload/contents.txt. For this task, check that the synonyms.txt file includes all genome versions supported by Galaxy. If not, update it. |
| Comment |
[ This ticket was first worked on in 2014 and needs to be re-visited because Galaxy code base has progressed and many new genome versions are available.
The Galaxy software relies heavily on the UCSC Genome Browser informatics system to support many different genome versions. There's a "cron job" that Galaxy admin's periodically run to update genome version data in Galaxy. We need to understand how that works to make sure that IGB's synonyms system stays up to date with Galaxy. The script(s) run during the cron job reside in: * https://github.com/galaxyproject/galaxy/tree/dev/cron The script in this directory that "kicks off" the update is updateucsc.sh.sample. It also handles getting length files with chromosome names and sizes. Note that this script also manages import of non-ucsc genome names. Look at the script to see how that aspect is working. The above is actually a legacy system but has been used for a long time and seems to work quite well. In addition, there's a "data manager" system that allows an admin to use the Galaxy UI to define new genomes. Each genome version is identified by a "dbkey" that in the case of ucsc genomes, is identical to ucsc genome version names. An example dbkey is "apiMel2", which is IGB, is called "A_mellifera_Jan_2005" Dan Blankenberg (https://galaxyproject.org/people/dan/) notes that there may actually be a REST endpoint that can report the dbkeys for all genome versions supported in a given Galaxy instance. If not, he recommends we open a ticket in Galaxy github requesting this. Galaxy also keeps track of a user-friendly name that is displayed to users. This is equivalent to column 2 in IGB Quickload's contents.txt file -- see http://igbquickload.org/quickload/contents.txt. For this task, check that the synonyms.txt file includes all genome versions supported by Galaxy. If not, update it. ] |
| Sprint | Summer 2019 Sprint 11 [ 70 ] | Summer 2019 Sprint 12 [ 71 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-1880 [ 17970 ] |
| Story Points | 0.5 | 2 |
| Rank | Ranked higher |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Sprint | Summer 2019 Sprint 12 [ 71 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1 [ 71, 72 ] |
| Rank | Ranked higher |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Workflow | Loraine Lab Workflow [ 18602 ] | Fall 2019 Workflow Update [ 19085 ] |
| Status | Reopened [ 4 ] | Open [ 1 ] |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1 [ 71, 72 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 71, 72, 73 ] |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 71, 72, 73 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 71, 72, 73, 74 ] |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3 [ 71, 72, 73, 74 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 2019 Sprint 4 [ 71, 72, 73, 74, 75 ] |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct [ 71, 72, 73, 74, 75 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 71, 72, 73, 74, 75, 76 ] |
| Rank | Ranked higher |
| Workflow | Fall 2019 Workflow Update [ 19085 ] | Revised Fall 2019 Workflow Update [ 20835 ] |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 71, 72, 73, 74, 75, 76 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 71, 72, 73, 74, 75, 76, 77 ] |
| Rank | Ranked higher |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 71, 72, 73, 74, 75, 76, 77 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 71, 72, 73, 74, 75, 76, 77, 78 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 71, 72, 73, 74, 75, 76, 77, 78 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 71, 72, 73, 74, 75, 76, 77, 78, 79 ] |
| Rank | Ranked higher |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
| Rank | Ranked higher |
| 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 ] | 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 ] |
| Link | This issue relates to IGBF-552 [ IGBF-552 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Nowlan Freese [ nfreese ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 71, 72, 73, 74, 75, 76, 77, 78, 79 ] | Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Spring 5 2021 May 17 - May 28 [ 71, 72, 73, 74, 75, 76, 77, 78, 79, 121 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] | Shamika Gajanan Kulkarni [ shamika ] |
| 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 ] |
