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  1. IGB
  2. IGBF-4386

Add Euphorbia lathyris genome to IGB Quickload

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          Situation: Dr. Camellia Okpodu of the University of Wyoming is studying the effects of herbicides on Euphorbia esula (leafy spurge), a noxious invasive weed. As of January 2026 there does not appear to be a good reference genome for leafy spurge (NCBI link), so Dr. Okpodu has aligned her data to Euphorbia lathyris (NCBI link).

          Task: Add Euphorbia lathyris and its annotation to IGB Quickload. Also, we're increasing scope to include adding this genome to the IGB carousel.

          Link: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_963576675.1/
          Note: Only the NCBI RefSeq assembly (GCF) includes the annotation, so please use that one.

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              Task - A task that needs to be done. IGBF-4408 Add Euphorbia lathyris image to IGB 10.3.0 home screen carousel

              • Major - Major loss of function.
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                ann.loraine Ann Loraine added a comment -

                Making a separate ticket for updating the IGB codebase with the image.

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                ann.loraine Ann Loraine added a comment - Making a separate ticket for updating the IGB codebase with the image.
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                ann.loraine Ann Loraine added a comment -

                Testing shows no problems, apart from the .htaccess file maybe needing to be updated, which I am going to investigate later.

                Moving to DONE!

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                ann.loraine Ann Loraine added a comment - Testing shows no problems, apart from the .htaccess file maybe needing to be updated, which I am going to investigate later. Moving to DONE!
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                ann.loraine Ann Loraine added a comment - - edited

                Web interface shows the new directory but there's no text next to the folder. Looks like the .htaccess file need to be updated? See: http://igbquickload.org/quickload/

                Even more folder names are missing at the main Quickload site: http://igbquickload-main.bioviz.org/quickload/

                I will make any necessary edits to the .htaccess file later because right now I want to set up a new Quickload site using the r233 backups.

                Apart from that, everything looks fantastic!

                Show
                ann.loraine Ann Loraine added a comment - - edited Web interface shows the new directory but there's no text next to the folder. Looks like the .htaccess file need to be updated? See: http://igbquickload.org/quickload/ Even more folder names are missing at the main Quickload site: http://igbquickload-main.bioviz.org/quickload/ I will make any necessary edits to the .htaccess file later because right now I want to set up a new Quickload site using the r233 backups. Apart from that, everything looks fantastic!
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                ann.loraine Ann Loraine added a comment - - edited

                I noticed the file permissions for the new content on the mirror site were messed up. I fixed them on site by manually logging in and running chmod command. I'm not sure what the deal is with that! The primary site (on RENCI) was fine, however.

                Show
                ann.loraine Ann Loraine added a comment - - edited I noticed the file permissions for the new content on the mirror site were messed up. I fixed them on site by manually logging in and running chmod command. I'm not sure what the deal is with that! The primary site (on RENCI) was fine, however.
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                ann.loraine Ann Loraine added a comment - - edited

                I updated the quickload sites available for IGB.

                To test:

                • Check that the new genome can be loaded from both the main site and the mirror site for IGB 10.2.0, the released version.
                • Check that the Web interfaces look right and the new genome files can be viewed and/or dowloaded in the web browser
                Show
                ann.loraine Ann Loraine added a comment - - edited I updated the quickload sites available for IGB. To test: Check that the new genome can be loaded from both the main site and the mirror site for IGB 10.2.0, the released version. Check that the Web interfaces look right and the new genome files can be viewed and/or dowloaded in the web browser
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                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    nfreese Nowlan Freese
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                      Updated:
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