Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2548

Investigate: Why do wheat gene models fail to load

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          See error report in IGBF-2333 for problem description.

            Attachments

              Issue Links

              relates to

              New Feature - A new feature of the product, which has yet to be developed. IGBF-2538 Support CSI tabix index for very large genomes

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2333 Add wheat genome to IGB quickload system

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2333 [ IGBF-2333 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2538 [ IGBF-2538 ]
                ann.loraine Ann Loraine made changes -
                Description See error report in IGBF-2333 for problem description.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                Modified quickload to not use a compressed file for reference genomes. Edited annots.xml as follows:

                <files>
  <file
    name="T_aestivum_Aug_2018.bed"
    title="Gene models"
    description="Gene models from Ensembl 48"
    url="T_aestivum_Aug_2018"
    load_hint="Whole Sequence"
    foreground="000000"
    name_size="14"
    show2tracks="true"
    direction_type="arrow"
  />
</files>

                This solved the problem.

                Show
                ann.loraine Ann Loraine added a comment - - edited Modified quickload to not use a compressed file for reference genomes. Edited annots.xml as follows: <files> <file name= "T_aestivum_Aug_2018.bed" title= "Gene models" description= "Gene models from Ensembl 48" url= "T_aestivum_Aug_2018" load_hint= "Whole Sequence" foreground= "000000" name_size= "14" show2tracks= " true " direction_type= "arrow" /> </files> This solved the problem.
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: