Add new tomato genome and annotations to IGB Quickload repository

Answer from YZ:

Dear Ann,
Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/).
Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable.
Best regards,
Yao

Asked YZ for mapping between ITAG 4.0 and ITAG 5.0 names:

Thank you very much Yao Zhou! I appreciate it! I downloaded the GO annotations just now and am starting to use them.

I have a quick followup question which I hope will not be too much trouble!

Do you have a spreadsheet that maps your new ITAG 5.0 names onto the older ITAG 4.0 (SL4.0 assembly) names?

Until new and improved gene descriptions are available for ITAG 5.0, I was thinking that using the old gene descriptions, where possible, would be an OK temporary substitute. So having a quick and easy way to perform the mapping would be super helpful.

Also, I wanted to let you know that I have released your wonderful new genome assembly and gene models in Integrated Genome Browser. Your new data looks great!

If, at some point, you and/or your colleagues would like a quick tour of the browser, I would be more than happy to show you

Warmest regards,

Ann

• Clicked tomato image in IGB release 9.1.8
• Tomato SL5.0 genome was loaded with ITAG5.0 gene models.
• Gene models were able to be loaded for all chromosomes.
• Genome version shows as S_lycopersicum_Jun_2022.
• Chromosomes show as 0-12 (this seems a little odd as the previous genome versions used SL#.0ch##)
• "i" icon reads as ITAG5.0 gene models, SL5.0 genome assembly (looks good).
• Clicking "i" icon opens the Quickload web page. Text makes sense.
• Parent directory shows "Solanum lycopersicum (Jun 2022) tomato (SL5.0)" for S_lycopersicum_Jun_2022/
• IGB Genomes includes new tomato genome version, correct genome in IGB is opened when clicked.
• BioViz Connect shows the new genome version as an option under metadata.

No issues encountered. Closing ticket.

To test:

• Open IGB
• Click tomato image on start screen to load latest genome version
• Observe SL5.0 is loaded - with gene models
• Hover mouse over the "i" in Data Access Panel. Check that the message makes sense.
• Click "i" in Data Access Panel. Check that the SL5.0 data directory on the Quickload host opens. Read the text. Check it makes sense.
• Navigate one directory higher (see previous step.) Check that S_lycopersicum_Jun_2022 has a description in the files and folder listing.

Also:

• Check that IGB Genomes link on BioViz.org Web site shows the new genome version and that IGB can open this when you click the version shown.
• Check that BioViz Connect also shows the new genome version as an option for annotating files.

Need to deploy new data to:

• http://igbquickload.org/quickload - hosted behind UNC Charlotte firewall - DONE
• http://lorainelab-quickload.scidas.org/quickload/ - hosted at RENCI - DONE
• https://quickload.bioviz.org - hosted at AWS - DONE

Discovered a problem with "data" directory on quickload.bioviz.org. Seems to have come unmounted. "data" directory is mounted volume vol-00695402d76f72259, listed in AWS console as attached to the EC2 host. Tried rebooting EC2. No change. Unmounted volume in console, then re-attached in console, rebooted. No change. Remounted with command "mount -t ext4 /dev/sdf /data". Able to then change into /data/quickload and run "svn up" as root user.

Logging in to UNC Charlotte VPN. Then executing alias "quickload" (ssh -J aloraine@cci-moss -p 1657 aloraine@igbquickload.org) to reach quickload host.