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  1. IGB 8.1
  2. IGBE-91

Test galaxy data access

          Details

          • Type: Bug
          • Status: Reopened (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Labels:
            None
          • Environment:

            6.7

            Description

            Support to deploy IGB directly from Galaxy has been implemented.
            To test the feature we need to
            *load an annotation file to galaxy
            *request to view the file using IGB.
            Do "scientific" things with the data to make sure the communication between galaxy and IGB does not break
            the same should be done with:
            *bam
            *bigbed
            *bed
            *bigwig
            *wig

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                12 older comments
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                kyle Kyle Suttlemyre (Inactive) added a comment -

                Answer for (1) they exist since galaxy can access them and they are persistent over restarts and sessions. I can download all 3 files and they are of equal size. Running md5checks on them vs the original end up being the same hash so the files are not becoming corrupt.

                Partial Answer for (2) IGB still hangs in downloading when using usegalaxy.org and the url looks like this

                http://localhost:7085/UnibrowControl?version=Arabidopsis_thaliana_TAIR10&feature_url_0=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&sym_name_0=GES1_bam&sym_method_0=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&query_url=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&server_url=galaxy

                server_url=galaxy is still the same on both usegalaxy.org and the local version.

                Answer for (3) version=? is that way because the local hosted version of galaxy does not have A. thal as a choice for reference genome. I can test around this by version=? from the link then manually opening A. Thal in IGB before clicking the IGB links above.

                The issue may be with suggestion (4) or (2) which I am working on currently

                Show
                kyle Kyle Suttlemyre (Inactive) added a comment - Answer for (1) they exist since galaxy can access them and they are persistent over restarts and sessions. I can download all 3 files and they are of equal size. Running md5checks on them vs the original end up being the same hash so the files are not becoming corrupt. Partial Answer for (2) IGB still hangs in downloading when using usegalaxy.org and the url looks like this http://localhost:7085/UnibrowControl?version=Arabidopsis_thaliana_TAIR10&feature_url_0=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&sym_name_0=GES1_bam&sym_method_0=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&query_url=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&server_url=galaxy server_url=galaxy is still the same on both usegalaxy.org and the local version. Answer for (3) version=? is that way because the local hosted version of galaxy does not have A. thal as a choice for reference genome. I can test around this by version=? from the link then manually opening A. Thal in IGB before clicking the IGB links above. The issue may be with suggestion (4) or (2) which I am working on currently
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                ann.loraine Ann Loraine added a comment -

                link labeled "local" in UseGalaxy.org for BA1 reads file (a BAM file)

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                ann.loraine Ann Loraine added a comment - link labeled "local" in UseGalaxy.org for BA1 reads file (a BAM file)
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                ann.loraine Ann Loraine added a comment -

                What wget printed when we tried to access the link (see attached) when IGB r16004 branch was running and showing A_thaliana_Jun_2009.

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                ann.loraine Ann Loraine added a comment - What wget printed when we tried to access the link (see attached) when IGB r16004 branch was running and showing A_thaliana_Jun_2009.
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                kyle Kyle Suttlemyre (Inactive) added a comment -

                David Norris is changing how Galaxy and IGB interact.

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                kyle Kyle Suttlemyre (Inactive) added a comment - David Norris is changing how Galaxy and IGB interact.
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                ann.loraine Ann Loraine added a comment - - edited

                Please review this old testing ticket and migrate information to our newer testing system for Galaxy. When that is done, please close.

                Note: The workflow attached to this from an older board.

                Show
                ann.loraine Ann Loraine added a comment - - edited Please review this old testing ticket and migrate information to our newer testing system for Galaxy. When that is done, please close. Note: The workflow attached to this from an older board.

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    alyssa Alyssa Gulledge (Inactive)
                  • Votes:
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                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated: