I've placed a zipped version of the new quickload folder in Google Drive for the reviewer to take a look at:
Path: research-big-lorainelab > IGB Project Documentation and Plans > IGB Genomes > A_albopictus.zip
Link: https://drive.google.com/drive/folders/1bFRx4PqldxNf400n7Vr9SD_dNeNmtpvk?usp=drive_link

Question for the reviewer: If there's no manuscript published which details more about the genome assembly and its annotations, is there any other info I should provide in HEADER.md for IGB Quickload users to reference?

Tested quickload folder on Mac.

Everything loaded correctly. Able to load sequence and the annotation file shows correctly. No errors in log. Header looks good to me, I don't think you need to add anything else.

One side note: I don't think we need the genus species (Aedes albopictus) in the second column of the synonyms.txt (see user's guide). I don't think it hurts anything, but I don't think we need to include it.

Ready to push to SVN repo.

Thanks, NF! I'll leave out genus species names for genome additions going forward.

The subversion repository appears to be down which is preventing me from pushing this quickload to the SVN site. When I try to check-in my changes, svn is responding with

svn: E200029: Commit failed (details follow):
svn: E200029: could not begin a transaction

And when I try to update my working copy with "svn update", svn is responding with

svn: E200029: Couldn't perform atomic initialization

Ann Loraine, could you restart the svn site and reattach the virtual hard drive storing the data like you did for IGBF-3748 and IGBF-3890?

The SVN site is back up and running, and the Aedes albopictus genome has been pushed to the SVN repo.

Ready for final review!

Tested using my local copy of the SVN repo.

Gene models load correctly, able to load sequence, synonyms/species look good, Header.md looks good.

Ready to be deployed.

Revision 225 of the svn repository is now deployed. Ready for final testing.

Request: Please check that the Web browser interface to the genome assembly directory on quickload makes sense and that all links work.

Tested on Mac with main branch installer.

• Aedes albopictus appears in the Species dropdown with the correct synonyms.
• Gene models and the sequence loads (2bit located at UCSC).
• Quickload page loads.
  • ISSUE - The ncbi link is not working. Because it is not a full URL the webpage assumes it is a relative path. Update to be a full path: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_035046485.1/
  • Note that this issue is also present for
    • Capitella teleta
    • Hydra vulgaris
    • Oryzias latipes
    • Vanessa cardui

I've pushed changes to the HEADER.md files for all of the above listed genomes. Dr. Loraine created a template HEADER.md file as part of IGBF-4038, so that is the new format I followed here. The SVN repository is now at revision 227. Ready for review!

Tested Header.md for the following genomes. All links are working correctly.

• Aedes albopictus
• Capitella teleta
• Hydra vulgaris
• Oryzias latipes
• Vanessa cardui

Ready to be deployed.

I have deployed the new repository to our hosting at RENCI (the default quickload site) and to our hosting at charlotte. Ready for final testing.

To test, I visited each page for the above listed genome versions, hosted on our QL site.

For example, the V. cardui quickload page is: http://igbquickload-main.bioviz.org/quickload/V_cardui_Feb_2021/

All the links worked.

Moving to Done.