Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3076

Get help and information from CyVerse regarding why the new app won't properly run

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          0.5
        • Epic Link:
        • Sprint:
          Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11, Spring 6 2022 Mar 14 - Mar 25, Spring 7 2022 Mar 28 - Apr 8

          Description

          Karthik Raveendran has created a new Docker image containing deepTools, tabix (samtools), and a custom script he wrote to enable running of the image in CyVerse environment to compute a scaled coverage graph file (bedgraph format) and then tabix-index it.

          He's run into some problems with getting the new image to run as wanted in the environment.

          He will send a email asking about this to the CyVerse team and record the answers and insights obtained here.

          Questions:

          • How do I get access to the condor stderr and stdout ?
          • How do I add metadata tags to my app even while it's in my private account and not yet widely available, i.e., "published"

          This may be helpful:

          IGB class information about using the IGB Docker image to build IGB:
          https://canvas.instructure.com/courses/1164217/pages/learn-to-use-igb-docker-image-build-environment?module_item_id=43241015

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3035 Create Cyverse App to create and index Bedgraph

              • 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
                Description [~karthik] has created a new Docker image containing deepTools, tabix (samtools), and a custom script he wrote to enable running of the image in CyVerse environment to compute a scaled coverage graph file (bedgraph format) and then tabix-index it.

                He's run into some problems with getting the new image to run as wanted in the environment.

                He will send a email asking about this to the CyVerse team and record the answers and insights obtained here.                 		[~karthik] has created a new Docker image containing deepTools, tabix (samtools), and a custom script he wrote to enable running of the image in CyVerse environment to compute a scaled coverage graph file (bedgraph format) and then tabix-index it.

                He's run into some problems with getting the new image to run as wanted in the environment.

                He will send a email asking about this to the CyVerse team and record the answers and insights obtained here.

                Questions:

                * How do I get access to the condor stderr and stdout ?
                * How do I add metadata tags to my app even while it's in my private account and not yet widely available, i.e., "published"
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-2376 [ 18533 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3035 [ IGBF-3035 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 2022 Jan 31 - Feb 11 [ 138 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 2022 Jan 31 - Feb 11 [ 138 ] Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 138, 139 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 138, 139 ] Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11 [ 138, 139, 140 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11 [ 138, 139, 140 ] Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11, Spring 6 2022 Mar 14 - Mar 25 [ 138, 139, 140, 141 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Description [~karthik] has created a new Docker image containing deepTools, tabix (samtools), and a custom script he wrote to enable running of the image in CyVerse environment to compute a scaled coverage graph file (bedgraph format) and then tabix-index it.

                He's run into some problems with getting the new image to run as wanted in the environment.

                He will send a email asking about this to the CyVerse team and record the answers and insights obtained here.

                Questions:

                * How do I get access to the condor stderr and stdout ?
                * How do I add metadata tags to my app even while it's in my private account and not yet widely available, i.e., "published"                 		[~karthik] has created a new Docker image containing deepTools, tabix (samtools), and a custom script he wrote to enable running of the image in CyVerse environment to compute a scaled coverage graph file (bedgraph format) and then tabix-index it.

                He's run into some problems with getting the new image to run as wanted in the environment.

                He will send a email asking about this to the CyVerse team and record the answers and insights obtained here.

                Questions:

                * How do I get access to the condor stderr and stdout ?
                * How do I add metadata tags to my app even while it's in my private account and not yet widely available, i.e., "published"


                This may be helpful:

                IGB class information about using the IGB Docker image to build IGB:
                https://canvas.instructure.com/courses/1164217/pages/learn-to-use-igb-docker-image-build-environment?module_item_id=43241015
                karthik Karthik Raveendran made changes -
                Attachment Argument.png [ 17209 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11, Spring 6 2022 Mar 14 - Mar 25 [ 138, 139, 140, 141 ] Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11, Spring 6 2022 Mar 14 - Mar 25, Spring 7 2022 Mar 28 - Apr 8 [ 138, 139, 140, 141, 142 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                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:
                    karthik Karthik Raveendran
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: