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  1. IGB
  2. IGBF-3680

Improve documentation: Explain how our FindJunctions is different from Top Hat find junctions feature

        Details

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

          Description

          There's currently no form of documentation in the User's Guide that I can find explaining the difference between FindJunctions (Top Hat) and Find Junctions. The only mention I can find of the former in the User's Guide is here in the IGB Gallery.

          Task: Investigate the difference between FindJunctions (Top Hat) and Find Junctions and report your findings on this ticket. Then, create a new ticket to do the following:

          • Either update the FindJunctions page of the User's Guide, or
          • Create a new page in the User's Guide detailing FindJunctions (Top Hat) and how to use it in IGB.

            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-1088 Update FindJunctions page in User's Guide

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

              Documentation - When documentation is missing or wrong IGBF-3679 Document instructions for compiling FindJunctions via Bitbucket

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

                Activity

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                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-1088 [ IGBF-1088 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 8 [ 192 ]
                ann.loraine Ann Loraine made changes -
                Summary Investigate: How does FindJunctions (Top Hat) differ from Find Junctions? Improve documentation: Explain how our FindJunctions is different from Top Hat find junctions feature
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                This will require asking Ann Loraine for the information required.

                Show
                ann.loraine Ann Loraine added a comment - This will require asking Ann Loraine for the information required.
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3679 [ IGBF-3679 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 9 [ 193 ]
                pkulzer Paige Kulzer made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9 [ 193 ] Spring 9, Spring 10 [ 193, 194 ]
                ann.loraine Ann Loraine 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 -
                Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3738 [ IGBF-3738 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Documentation is updated and ready for review.

                Show
                ann.loraine Ann Loraine added a comment - Documentation is updated and ready for review.
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
                Permalink
                pkulzer Paige Kulzer added a comment -

                The difference between FindJunctions and FindJunctions (TopHat) has been explained in the documentation, and a link to the TopHat manual has been provided which will help user's better familiarize themselves with the program.

                Small suggestion for Ann Loraine: Move the second picture so that it's directly underneath the instructions to run FindJunctions since it is most relevant to those steps.

                Moving this to Merged, Needs Review for Dr. Loraine to look over the suggestion and decide if she'd like to implement it.

                Show
                pkulzer Paige Kulzer added a comment - The difference between FindJunctions and FindJunctions (TopHat) has been explained in the documentation, and a link to the TopHat manual has been provided which will help user's better familiarize themselves with the program. Small suggestion for Ann Loraine : Move the second picture so that it's directly underneath the instructions to run FindJunctions since it is most relevant to those steps. Moving this to Merged, Needs Review for Dr. Loraine to look over the suggestion and decide if she'd like to implement it.
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pkulzer Paige Kulzer made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                pkulzer Paige Kulzer made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Update:

                • I added an image. Image file is in Dropbox / IGB Users Guide
                • Made the new image by adding the image file and callouts to a KeyNote document also in Dropbox / IGB Users Guide (KeyNote is slide show editing software from Apple)
                • Moving back to "To-Do" for one more copy-editing check
                Show
                ann.loraine Ann Loraine added a comment - Update: I added an image. Image file is in Dropbox / IGB Users Guide Made the new image by adding the image file and callouts to a KeyNote document also in Dropbox / IGB Users Guide (KeyNote is slide show editing software from Apple) Moving back to "To-Do" for one more copy-editing check
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9, Spring 10 [ 193, 194 ] Spring 9, Spring 10, Summer 1 [ 193, 194, 195 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                pkulzer Paige Kulzer added a comment -

                I've found the new images in Dropbox (Dropbox > IGB Users Guide Art and Style Info > FindJunctions) and see that the FindJunctions page in the user's guide has been updated accordingly.

                Another change request: The instructions for compiling FindJunctions on BitBucket list six optional arguments that FindJunctions jar accepts, but the user's guide only lists four. Please update the FindJunctios page in the user's guide so that all six optional arguments are listed there.

                Show
                pkulzer Paige Kulzer added a comment - I've found the new images in Dropbox (Dropbox > IGB Users Guide Art and Style Info > FindJunctions) and see that the FindJunctions page in the user's guide has been updated accordingly. Another change request : The instructions for compiling FindJunctions on BitBucket list six optional arguments that FindJunctions jar accepts, but the user's guide only lists four. Please update the FindJunctios page in the user's guide so that all six optional arguments are listed there.
                pkulzer Paige Kulzer made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Removed CLI FindJunctions documentation from the wiki because it is redundant with the bitbucket site and replaced it with text letting the user know they can visit the bitbucket site for information on how to run FindJunctions as a command-line program.

                Show
                ann.loraine Ann Loraine added a comment - Removed CLI FindJunctions documentation from the wiki because it is redundant with the bitbucket site and replaced it with text letting the user know they can visit the bitbucket site for information on how to run FindJunctions as a command-line program.
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
                Hide
                Permalink
                pkulzer Paige Kulzer added a comment -

                Thank you for that change! The FindJunctions page in the user's guide looks complete to me now. Moving this ticket to Done.

                Show
                pkulzer Paige Kulzer added a comment - Thank you for that change! The FindJunctions page in the user's guide looks complete to me now. Moving this ticket to Done.
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pkulzer Paige Kulzer made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                pkulzer Paige Kulzer made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    pkulzer Paige Kulzer
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                    Dates

                    • Created:
                      Updated:
                      Resolved: