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  1. IGB
  2. IGBF-2911

Handle araTha1 synonym in track hub facade

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        • Story Points:
          0.5
        • Epic Link:
        • Sprint:
          Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24

          Description

          The JASPAR TFBS track hub appears to have data for the Arabidopsis thaliana genome, but uses a name that IGB does not currently recognize: "araTha1".

          For this task, we need to figure out what the corresponding IGB name is and add it to IGB's synonyms system, or provide the synonym within the track hub synonyms endpoint.

          (See attached image.)

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              Task - A task that needs to be done. IGBF-2954 Investigate: why is loading bb (bigbed) and bigwig (bw) files so slow?

              • Major - Major loss of function.
              • Closed

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                6 older comments
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                Did you make the changes I describe near the end of this previous comment?

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                pbadzuh Philip Badzuh (Inactive) added a comment - Did you make the changes I describe near the end of this previous comment ?
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                ann.loraine Ann Loraine added a comment -

                Sorry, I did not. Working on it.

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                ann.loraine Ann Loraine added a comment - Sorry, I did not. Working on it.
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                ann.loraine Ann Loraine added a comment -

                Build and ran new version of IGB from this branch: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2911?dest=master

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                ann.loraine Ann Loraine added a comment - Build and ran new version of IGB from this branch: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2911?dest=master
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                ann.loraine Ann Loraine added a comment -

                Adding the new synonym enables IGB to access the JASPAR track hub. However, all the data files appear to load extremely slowly, even when I zoom in and click "Load Data" for a smaller region.
                I tried downloading one of the files directly onto my computer, and it will take probably around 15 minutes or longer for the file to download.
                (This is the file URL: http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb)
                Is the "bigbed" format being handled the way it should in IGB, with the index from the top of the file getting loaded first followed by a second request to retrieve precisely the data needed? Will make a separate issue for this. For now, will merge in the new synonym update to the main development branch and move this ticket to closed.

                Show
                ann.loraine Ann Loraine added a comment - Adding the new synonym enables IGB to access the JASPAR track hub. However, all the data files appear to load extremely slowly, even when I zoom in and click "Load Data" for a smaller region. I tried downloading one of the files directly onto my computer, and it will take probably around 15 minutes or longer for the file to download. (This is the file URL: http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/JASPAR2022_araTha1.bb ) Is the "bigbed" format being handled the way it should in IGB, with the index from the top of the file getting loaded first followed by a second request to retrieve precisely the data needed? Will make a separate issue for this. For now, will merge in the new synonym update to the main development branch and move this ticket to closed.
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                ann.loraine Ann Loraine added a comment -

                Merged into IGB master branch (POM version 9.1.10). Moving to Done.

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                ann.loraine Ann Loraine added a comment - Merged into IGB master branch (POM version 9.1.10). Moving to Done.

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                      Updated:
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