Details
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Type:
New Plugin
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.8 Major Release
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Labels:
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Story Points:3
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Epic Link:
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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.
Attachments
Issue Links
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IGBF-2805 Describe how to test the feature of adding and using a local quickload on Windows, Mac, Linux to Release Testing.
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- Closed
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- relates to
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IGBF-2737 Test Quickload Saver App on Windows, Mac and Linux
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- Closed
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IGBF-2738 Review workflow for installing Quickload Saver App using App Store
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- Closed
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IGBF-2785 Update POM to include micro version
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- Closed
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IGBF-3108 Release Create Quickload App on App Store
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- Closed
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IGBF-3206 Investigate: In Quickload Saver, saving custom quickload does not use native file chooser
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- To-Do
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IGBF-2783 Improve Open Genome from File UI
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- Closed
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IGBF-2804 Output species.txt in the Quickload Saver app
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- Closed
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IGBF-2822 Edit don't over-write contents.txt in Quickload Saver
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- To-Do
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Activity
[~aloraine] - By creating a quickload, do you mean to just put all the 3 meta-data files in the folder the user chooses?
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.