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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.

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              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 added a comment -

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

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                nfreese Nowlan Freese added a comment - See IGBF-1217 for additional information on storing a Quickload on Bitbucket.
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                nfreese Nowlan Freese added a comment -

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

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

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

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                nfreese Nowlan Freese added a comment - The next step will be to upload the data files to the BioViz community folder in CyVerse.
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                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/

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                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/
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                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

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                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
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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.
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                nfreese Nowlan Freese added a comment -

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

                Closing ticket.

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                nfreese Nowlan Freese added a comment - All data load correctly in the track hub. The Readme has been updated. Closing ticket.

                  People

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

                    • Created:
                      Updated:
                      Resolved: