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  1. IGB
  2. IGBF-1879

Ensure Galaxy default dbkey values are in synonyms.txt

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          2
        • Epic Link:
        • 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

              blocks

              Task - A task that needs to be done. IGBF-2849 Release IGB 9.1.8

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-4112 2025 Update Galaxy dbkey values in IGB synonyms.txt

              • Major - Major loss of function.
              • To-Do

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2862 Fix loading bookmark from Galaxy when genome from UCSC

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-781 Update synonyms.txt for UCSC

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                dcnorris David Norris (Inactive) created issue -
                dcnorris David Norris (Inactive) made changes -
                Field Original Value New Value
                Status Open [ 1 ] Resolved [ 5 ]
                Resolution Fixed [ 1 ]
                dcnorris David Norris (Inactive) made changes -
                Status Resolved [ 5 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Resolution Fixed [ 1 ]
                Status Closed [ 6 ] Reopened [ 4 ]
                Assignee David Norris [ dcnorris ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.5
                Sprint Summer 2019 Sprint 11 [ 70 ]
                Labels Intermediate
                ann.loraine Ann Loraine made changes -
                Project IGB 8.1 [ 10640 ] IGB [ 10840 ]
                Key IGBE-142 IGBF-1879
                Workflow classic default workflow [ 14357 ] Loraine Lab Workflow [ 18602 ]
                ann.loraine Ann Loraine made changes -
                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.

                ann.loraine Ann Loraine made changes -
                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.

                ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2019 Sprint 11 [ 70 ] Summer 2019 Sprint 12 [ 71 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1880 [ 17970 ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.5 2
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Assignee Shamika Gajanan Kulkarni [ shamika ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2019 Sprint 12 [ 71 ] Summer 2019 Sprint 12, Fall 2019 Sprint 1 [ 71, 72 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Shamika Gajanan Kulkarni [ shamika ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18602 ] Fall 2019 Workflow Update [ 19085 ]
                Status Reopened [ 4 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19085 ] Revised Fall 2019 Workflow Update [ 20835 ]
                Status Open [ 1 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Assignee Shamika Gajanan Kulkarni [ shamika ]
                shamika Shamika Gajanan Kulkarni (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                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 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-781 [ IGBF-781 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-552 [ IGBF-552 ]
                nfreese Nowlan Freese made changes -
                Assignee Shamika Gajanan Kulkarni [ shamika ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                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 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2862 [ IGBF-2862 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Shamika Gajanan Kulkarni [ shamika ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-2849 [ IGBF-2849 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-4112 [ IGBF-4112 ]

                  People

                  • Assignee:
                    shamika Shamika Gajanan Kulkarni (Inactive)
                    Reporter:
                    dcnorris David Norris (Inactive)
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                      Updated:
                      Resolved:

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