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  1. IGB
  2. IGBF-1623

Implement DepthGraph App in CyVerse

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Epic Link:
        • Sprint:
          Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3

          Description

          Situation: Aim 4 of the IGB-CyVerse grant uses an example app to make a coverage graph from a BAM file using CyVerse HPC infrastructure.

          Tasks:
          Investigate the current apps/tools available through the Discovery Environment.
          Determine if any current tools/apps would be sufficient.
          If a tool/app is sufficient, implement it in the Discovery Environment.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-1811 Investigate DE Analysis Apps

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1482 [ 17568 ]
                nfreese Nowlan Freese made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ] Spring 2019 Sprint 3 [ 61 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 5 [ 61, 63 ]
                nfreese Nowlan Freese made changes -
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                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 5 [ 61, 63 ] Spring 2019 Sprint 3 [ 61 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 6 [ 61, 64 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 6 [ 61, 64 ] Spring 2019 Sprint 3 [ 61 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 7 [ 61, 66 ]
                nfreese Nowlan Freese made changes -
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                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 7 [ 61, 66 ] Spring 2019 Sprint 3 [ 61 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8 [ 61, 67 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8 [ 61, 67 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 61, 67, 68 ]
                ann.loraine Ann Loraine made changes -
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                nfreese Nowlan Freese made changes -
                Summary Investigate DepthGraph App in CyVerse Implement DepthGraph App in CyVerse
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1811 [ IGBF-1811 ]
                nfreese Nowlan Freese made changes -
                Description Situation: Aim 4 of the IGB-CyVerse grant uses an example app to make a coverage graph from a BAM file using CyVerse HPC infrastructure.

                Tasks:
                Investigate the current apps/tools available through the Discovery Environment and/or Agave API.
                Determine if any current tools/apps would be sufficient.
                If a tool/app is sufficient, write up documentation for it, otherwise create a new JIRA issue with the task of developing a tool/app to create a coverage graph.                 		Situation: Aim 4 of the IGB-CyVerse grant uses an example app to make a coverage graph from a BAM file using CyVerse HPC infrastructure.

                Tasks:
                Investigate the current apps/tools available through the Discovery Environment.
                Determine if any current tools/apps would be sufficient.
                If a tool/app is sufficient, implement it in the Discovery Environment.
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                nfreese Nowlan Freese added a comment -

                I have implemented a bedtools genomecov app in the DE that will produce a coverage graph in bedgraph format. The app is currently not public, as it requires some additional testing (paired-end data) and updated documentation within the DE before being made public (once public no additional edits can be made). This tool may also be superseded by a deeptools bamcoverage app, however I am still waiting for DE staff to add the tool.

                Show
                nfreese Nowlan Freese added a comment - I have implemented a bedtools genomecov app in the DE that will produce a coverage graph in bedgraph format. The app is currently not public, as it requires some additional testing (paired-end data) and updated documentation within the DE before being made public (once public no additional edits can be made). This tool may also be superseded by a deeptools bamcoverage app, however I am still waiting for DE staff to add the tool.
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 61, 67, 68 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8 [ 61, 67 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8 [ 61, 67 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10 [ 61, 67, 69 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status Open [ 1 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
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                nfreese Nowlan Freese added a comment - - edited

                I have moved this to first level review. Currently only members of the CyVerse team will have access to this tool (as it cannot be made public yet).

                To Test:
                Upload the example BAM and index to your CyVerse DE.
                If you are a CyVerse team member, the tool "IGB Bedtools Genome Coverage" should be shared with you.
                Run the analysis using the DE UI or Postman (see the Terrain API documentation).
                Load the same example BAM file in IGB, and generate a depth graph .
                Load the bedgraph generated in CyVerse into IGB.
                The graphs should be the same (human genome (HG38) on chromosome 3).

                Show
                nfreese Nowlan Freese added a comment - - edited I have moved this to first level review. Currently only members of the CyVerse team will have access to this tool (as it cannot be made public yet). To Test: Upload the example BAM and index to your CyVerse DE. If you are a CyVerse team member, the tool "IGB Bedtools Genome Coverage" should be shared with you. Run the analysis using the DE UI or Postman (see the Terrain API documentation). Load the same example BAM file in IGB, and generate a depth graph . Load the bedgraph generated in CyVerse into IGB. The graphs should be the same (human genome (HG38) on chromosome 3).
                nfreese Nowlan Freese made changes -
                Attachment babyBam.bam [ 14369 ]
                Attachment babyBam.bam.bai [ 14370 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10 [ 61, 67, 69 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11 [ 61, 67, 69, 70 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11 [ 61, 67, 69, 70 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12 [ 61, 67, 69, 70, 71 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12 [ 61, 67, 69, 70, 71 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1 [ 61, 67, 69, 70, 71, 72 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18344 ] Fall 2019 Workflow Update [ 18961 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1 [ 61, 67, 69, 70, 71, 72 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 61, 67, 69, 70, 71, 72, 73 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2 [ 61, 67, 69, 70, 71, 72, 73 ] Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 61, 67, 69, 70, 71, 72, 73, 74 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Status Open [ 1 ] To-Do [ 10305 ]
                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 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 18961 ] Revised Fall 2019 Workflow Update [ 22208 ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: