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  1. IGB
  2. IGBF-2142

Link IGB to Galaxy

        Details

        • Type: New Feature
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Fixed
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Link up IGB to Galaxy so that Galaxy users can display their "BAM" files in IGB without first having to download them.

            Attachments

            1. bb.xml
              3 kB
            2. bb.xml
              0.7 kB
            3. bed.xml
              4 kB
            4. bigwig.xml
              4 kB

              Issue Links

              relates to

              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 -
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                hiralv Hiral Vora (Inactive) added a comment -

                Done.

                Show
                hiralv Hiral Vora (Inactive) added a comment - Done.
                hiralv Hiral Vora (Inactive) made changes -
                Field Original Value New Value
                Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                hiralv Hiral Vora (Inactive) made changes -
                Attachment bed.xml [ 10389 ]
                Attachment bb.xml [ 10390 ]
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                hiralv Hiral Vora (Inactive) added a comment - - edited

                Attached are xml file required by Galaxy. Bed works fine but BigBed doesn't work. Task is: get BigBed to work.

                Show
                hiralv Hiral Vora (Inactive) added a comment - - edited Attached are xml file required by Galaxy. Bed works fine but BigBed doesn't work. Task is: get BigBed to work.
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Hiral Vora [ hiralv ] Jeremy Villalobos [ jfvillal ]
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                ann.loraine Ann Loraine added a comment -

                We will need to test with Alyssa and/or Ann to check everything is working. If BigBed is fixed, BigWig will also be fixed.
                Before we submit the XML files to Galaxy project we need to test them first.

                Show
                ann.loraine Ann Loraine added a comment - We will need to test with Alyssa and/or Ann to check everything is working. If BigBed is fixed, BigWig will also be fixed. Before we submit the XML files to Galaxy project we need to test them first.
                Hide
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                jfvillal jfvillal added a comment -

                The attached files enable IGB deployment from Galaxy. The HTTP container must support seekable downloads. This note is included with the files as well.

                Show
                jfvillal jfvillal added a comment - The attached files enable IGB deployment from Galaxy. The HTTP container must support seekable downloads. This note is included with the files as well.
                jfvillal jfvillal made changes -
                Attachment bb.xml [ 10399 ]
                Attachment bigwig.xml [ 10400 ]
                jfvillal jfvillal made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                Permalink
                jfvillal jfvillal logged work - 04/Nov/11 12:42 PM
                • Time Spent:
                  4 days
                   
                  <No comment>
                jfvillal jfvillal made changes -
                issue.field.resolutiondate 2011-11-04 16:49:17.0 2011-11-04 16:49:17.959
                Remaining Estimate 0 minutes [ 0 ]
                Time Spent 4 days [ 115200 ]
                Worklog Id 10012 [ 10012 ]
                jfvillal jfvillal made changes -
                Status In Progress [ 3 ] Resolved [ 5 ]
                Resolution Fixed [ 1 ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Resolution Fixed [ 1 ]
                Status Resolved [ 5 ] Reopened [ 4 ]
                Assignee Jeremy Villalobos [ jfvillal ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Status Reopened [ 4 ] Closed [ 6 ]
                Resolution Fixed [ 1 ]
                ann.loraine Ann Loraine made changes -
                Project IGB6.6 [ 10021 ] IGB [ 10840 ]
                Key IGBA-34 IGBF-2142
                Workflow classic default workflow [ 10273 ] Revised Fall 2019 Workflow Update [ 23024 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1880 [ 17970 ]
                ann.loraine Ann Loraine made changes -
                Assignee Hiral Vora [ hiralv ]
                pkulzer Paige Kulzer (Inactive) made changes -
                Link This issue relates to IGBF-4011 [ IGBF-4011 ]

                  People

                  • Assignee:
                    hiralv Hiral Vora (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    0 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved:

                      Time Tracking

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                      Time Spent - 4 days
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