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  1. IGB
  2. IGBF-3125

Deploy human trackhub metadata on bitbucket

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: Trackhubs require several metadata files to work properly, similar to quickloads. The example human trackhub is currently deployed on CyVerse under Philip Badzuh's account at https://data.cyverse.org/dav-anon/iplant/home/pbadzuh/human_hub/. However, as Philip has graduated we would like to deploy the metadata files somewhere we can provide additional access.

          Task: Deploy the example human trackhub on Bitbucket. In addition, we need to deploy the bigBed and bigWig files also located on Philip's CyVerse account. A potential option is the BioViz community data folder on CyVerse.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3066 Create Track Hub for our human genome Quickload data

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1217 add Genome in a Bottle data sets to IGB Quickload

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-2831 [ 19524 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3066 [ IGBF-3066 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1217 [ IGBF-1217 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                See IGBF-1217 for additional information on storing a Quickload on Bitbucket.

                Show
                nfreese Nowlan Freese added a comment - See IGBF-1217 for additional information on storing a Quickload on Bitbucket.
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                The Bitbucket repo containing the Track Hub metadata is: https://bitbucket.org/nfreese/trackhub-human-hub/src/main/

                Show
                nfreese Nowlan Freese added a comment - The Bitbucket repo containing the Track Hub metadata is: https://bitbucket.org/nfreese/trackhub-human-hub/src/main/
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                The next step will be to upload the data files to the BioViz community folder in CyVerse.

                Show
                nfreese Nowlan Freese added a comment - The next step will be to upload the data files to the BioViz community folder in CyVerse.
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Data have been uploaded to the BioViz Community folder at the following URL: https://data.cyverse.org/dav-anon/iplant/home/shared/BioViz/track_hub/

                Show
                nfreese Nowlan Freese added a comment - Data have been uploaded to the BioViz Community folder at the following URL: https://data.cyverse.org/dav-anon/iplant/home/shared/BioViz/track_hub/
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                The Track Hub URL for the bitbucket repo is: https://bitbucket.org/nfreese/trackhub-human-hub/raw/main/hub.txt

                Show
                nfreese Nowlan Freese added a comment - The Track Hub URL for the bitbucket repo is: https://bitbucket.org/nfreese/trackhub-human-hub/raw/main/hub.txt
                Hide
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                nfreese Nowlan Freese added a comment -

                The final steps to complete this ticket are to edit the Readme and test that all of the data are able to be loaded in UCSC.

                Show
                nfreese Nowlan Freese added a comment - The final steps to complete this ticket are to edit the Readme and test that all of the data are able to be loaded in UCSC.
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 1 2022 May 23 [ 147 ] Summer 1 2022 May 23, Summer 2 2022 June 6 [ 147, 148 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                All data load correctly in the track hub. The Readme has been updated.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - All data load correctly in the track hub. The Readme has been updated. Closing ticket.
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                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 -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                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 -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Comment [ Steps to view this on UCSC needs more detail to avoid blockers when users visit UCSC pages and can't figure out what to do because the page has a lot of features and it's hard to know what the next step should be.

                We also need some slides or images describing how it looks when everything is working correctly. Creating these slides & images should be part of first level review / testing. ]
                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 ]
                ann.loraine Ann Loraine made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 9.1.10 Major Release [ 10700 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 9.1.10 Major Release [ 10700 ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: