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  1. IGB
  2. IGBF-3679

Document instructions for compiling FindJunctions via Bitbucket

        Details

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

          Description

          In the "Using FindJuctions from the command line" section from the Find Junctions page of the user's guide (linked here), it says, "Follow the instructions to compile FindJunctions and create a "jar" file." However, there are currently no instructions present in the FindJunctions repo on Bitbucket.

          Task: Add instructions for how a user can compile FindJunctions and create a "jar" file to the README file in the FindJunctions repo.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3738 Update find junctions repo even more - main branch, bitbucket pipeline, more readme text

              • Major - Major loss of function.
              • Closed

              Documentation - When documentation is missing or wrong IGBF-3680 Improve documentation: Explain how our FindJunctions is different from Top Hat find junctions feature

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

              Documentation - When documentation is missing or wrong IGBF-1088 Update FindJunctions page in User's Guide

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

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                5 older comments
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                nfreese Nowlan Freese added a comment -

                I am able to build FindJunctions using mvn and then run the runFJ.sh to produce a bed file. I am also able to create a bed file using the FindJunction_exe.jar.

                Ready for pull request.

                Show
                nfreese Nowlan Freese added a comment - I am able to build FindJunctions using mvn and then run the runFJ.sh to produce a bed file. I am also able to create a bed file using the FindJunction_exe.jar. Ready for pull request.
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                jsirigin Jaya Sravani Sirigineedi added a comment -

                Raised pull request: https://bitbucket.org/lorainelab/findjunctions/pull-requests/1. Please review and let me know if there are any issues.

                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - Raised pull request: https://bitbucket.org/lorainelab/findjunctions/pull-requests/1 . Please review and let me know if there are any issues.
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                ann.loraine Ann Loraine added a comment -

                Small change request:

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                ann.loraine Ann Loraine added a comment - Small change request: Please remove this repository reference from the POM: http://eos.transvar.org/nexus/content/repositories/freehep-maven/
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                jsirigin Jaya Sravani Sirigineedi added a comment -

                Updated Ann Loraine. Tested it again, it's working as expected. https://bitbucket.org/lorainelab/findjunctions/pull-requests/1

                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - Updated Ann Loraine . Tested it again, it's working as expected. https://bitbucket.org/lorainelab/findjunctions/pull-requests/1
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                ann.loraine Ann Loraine added a comment -

                The PR is merged, but the bitbucket pipeline failed, due to the need to update the JDK being used by the pipeline.
                I made a new issue to address this. See linked ticket.

                Show
                ann.loraine Ann Loraine added a comment - The PR is merged, but the bitbucket pipeline failed, due to the need to update the JDK being used by the pipeline. I made a new issue to address this. See linked ticket.

                  People

                  • Assignee:
                    jsirigin Jaya Sravani Sirigineedi
                    Reporter:
                    pkulzer Paige Kulzer
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                    Dates

                    • Created:
                      Updated:
                      Resolved: