Uploaded image for project: 'IGB 8.1'
  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

                  Descending order - Click to sort in ascending order
                  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.
                  Hide
                  Permalink
                  ann.loraine Ann Loraine added a comment -

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

                  Show
                  ann.loraine Ann Loraine added a comment - See attached file for example gtf file generated by cufflinks in Galaxy.

                    People

                    • Assignee:
                      kyle Kyle Suttlemyre (Inactive)
                      Reporter:
                      ann.loraine Ann Loraine
                    • Votes:
                      0 Vote for this issue
                      Watchers:
                      0 Start watching this issue

                      Dates

                      • Created:
                        Updated:
                        Resolved: