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    • Story Points:
      3
    • Sprint:
      Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2

      Description

      IGB makes it possible for users to visualize "custom genomes," which are genomes where they have used their own reference genome and visualized their own data files.

      Please see this User's Guide page for guidance on how this features works from the user's perspective:

      https://wiki.transvar.org/pages/viewpage.action?pageId=23200542

      Unfortunately, each time a user needs to use their "custom genome," they have to repeat the entire process described in the wiki.

      Instead of making them do this every time, let's implement a way for them to save their custom genome between sessions.

      How this could work:

      • Users will do the same thing as now when opening their custom genome.
      • We will create a new submenu option under the "File" menu that says "Save Custom Genome to Local Quickload Site"
      • When they choose that option, a popup will appear that asks the user to select a folder in the file system
      • Once they do that, IGB creates a quickload site consisting of meta-data files only - contents.txt, genome.txt, annots.xml
      • The annots.xml file tag "file" attribute will point to the local (or remote) files the user has loaded into IGB

      Note that thanks to the new "reference" file tag implemented in IGB 9.1.6, the reference sequence no longer has to reside in the same folder as the Quickload site, as was previously the case.

        Issue Links

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          Hide
          aloraine Ann Loraine added a comment - - edited

          Installers are built.
          Kindly test by downloading and installing the master branch installers for Windows and MacOS from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/.

          Show
          aloraine Ann Loraine added a comment - - edited Installers are built. Kindly test by downloading and installing the master branch installers for Windows and MacOS from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/ .
          Hide
          rweidenh Rachel Weidenhammer added a comment -

          I tested the Quickload Saver app on Windows using the latest bitbucket installer for IGB as part of my testing for IGBF-2737. Everything worked as described in the testing documentation.

          Show
          rweidenh Rachel Weidenhammer added a comment - I tested the Quickload Saver app on Windows using the latest bitbucket installer for IGB as part of my testing for IGBF-2737 . Everything worked as described in the testing documentation.
          Hide
          aloraine Ann Loraine added a comment -

          Chester Dias - kindly test on Linux platform.

          Show
          aloraine Ann Loraine added a comment - Chester Dias - kindly test on Linux platform.
          Hide
          nfreese Nowlan Freese added a comment -

          To test:
          Follow instructions here: https://wiki.transvar.org/display/ITD/Quickload+Saver

          Show
          nfreese Nowlan Freese added a comment - To test: Follow instructions here: https://wiki.transvar.org/display/ITD/Quickload+Saver
          Hide
          cdias1 Chester Dias added a comment -

          Testing completed as per the wiki on Ubuntu 20.04.1 LTS version. The overall functionalities seem to work as expected except for a minor issue mentioned below.

          When saving the custom genome locally, after navigating to the folder where we want to save it to if we simply press the save button of the dialog box without giving a name the dialog box closes , but creates a folder with a random name sometimes genome version is the name.

          Show
          cdias1 Chester Dias added a comment - Testing completed as per the wiki on Ubuntu 20.04.1 LTS version. The overall functionalities seem to work as expected except for a minor issue mentioned below. When saving the custom genome locally, after navigating to the folder where we want to save it to if we simply press the save button of the dialog box without giving a name the dialog box closes , but creates a folder with a random name sometimes genome version is the name.

            People

            • Assignee:
              nfreese Nowlan Freese
              Reporter:
              mason Mason Meyer
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