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  1. IGB 8.1
  2. IGBE-150

add support for GTF to Galaxy

          Details

          • Type: Improvement
          • Status: Resolved (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None

            Description

            When users run Cufflinks on a BAM file in Galaxy, it generates a "GTF" file. IGB is able to open and display the contents of these files. Please add an XML file to Galaxy that will activate IGB view links for GTF format files. The extension of such files will be "gtf". See linked issue's attachments for an example gtf file you can upload to your test Galaxy instance for testing.

              Attachments

                Issue Links

                relates to

                Bug - A problem which impairs or prevents the functions of the product. IGBE-149 correct default styles not being set for GTF

                • Major - Major loss of function.
                • Resolved

                Task - A task that needs to be done. IGBF-4011 Enable IGB to open Galaxy CRAM format data sets

                • Major - Major loss of function.
                • Closed

                  Activity

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                  ann.loraine Ann Loraine created issue -
                  ann.loraine Ann Loraine made changes -
                  Field Original Value New Value
                  Assignee Ann Loraine [ aloraine ] David Norris [ dcnorris ]
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                  ann.loraine Ann Loraine added a comment -

                  See attached file for example gtf file generated by cufflinks in Galaxy.

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                  ann.loraine Ann Loraine added a comment - See attached file for example gtf file generated by cufflinks in Galaxy.
                  ann.loraine Ann Loraine made changes -
                  Link This issue relates to IGBE-149 [ IGBE-149 ]
                  ann.loraine Ann Loraine made changes -
                  Description When users run Cufflinks on a BAM file in Galaxy, it generates a "GTF" file. IGB is able to open and display the contents of these files. Please add an XML file to Galaxy that will activate IGB view links for GTF format files. The extension of such files will be "gtf". When users run Cufflinks on a BAM file in Galaxy, it generates a "GTF" file. IGB is able to open and display the contents of these files. Please add an XML file to Galaxy that will activate IGB view links for GTF format files. The extension of such files will be "gtf". See linked issue's attachments for an example gtf file you can upload to your test Galaxy instance for testing.
                  Hide
                  Permalink
                  dcnorris David Norris (Inactive) added a comment -

                  Added: Commit Hash - 664119e9a710391b8fbd50f1dce71502e3cd7703

                  Available for testing from test.bioviz.org and integrated into our test galaxy instance.

                  Show
                  dcnorris David Norris (Inactive) added a comment - Added: Commit Hash - 664119e9a710391b8fbd50f1dce71502e3cd7703 Available for testing from test.bioviz.org and integrated into our test galaxy instance.
                  dcnorris David Norris (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee David Norris [ dcnorris ] Kyle Suttlemyre [ kyle ]
                  Resolution Fixed [ 1 ]
                  ann.loraine Ann Loraine made changes -
                  Epic Link IGBF-1880 [ 17970 ]
                  pkulzer Paige Kulzer (Inactive) made changes -
                  Link This issue relates to IGBF-4011 [ IGBF-4011 ]

                    People

                    • Assignee:
                      kyle Kyle Suttlemyre (Inactive)
                      Reporter:
                      ann.loraine Ann Loraine
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                      Dates

                      • Created:
                        Updated:
                        Resolved: