Below is an outline of the steps I followed to create the Oryzias latipes Quickload:

1. Use wget to obtain the .2bit file from the UCSC Genome Bioinformatics website, then rename it

brew install wget
wget https://hgdownload.soe.ucsc.edu/hubs/GCF/002/234/675/GCF_002234675.1/GCF_002234675.1.2bit
mv GCF_002234675.1.2bit O_latipes_Jul_2017.2bit

2. Create genome.txt

./twoBitInfo O_latipes_Jul_2017.2bit genome.txt

3. Use Oryzias latipes' taxID (8090) to get the information we need from gene2accession.gz and gene_info.gz to create the BED14 file in a later step

gunzip -c gene2accession.gz | grep '^8090\t' > 8090.gene2accession.txt
gunzip -c gene_info.gz | grep '^8090\t' > 8090.gene_info.txt

4. Set up Python2 (if not already done so) in order to run the script in the next step

brew install pyenv
pyenv install 2.7.18

In your .bash_profile (or zshell/zshrc) add the following:

##Set path for pyenv
export PYENV_ROOT="$HOME/.pyenv"
[[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"

Then run this:

pyenv shell 2.7.18

5. Download the BED file from UCSC's table browser (Link: https://genome.ucsc.edu/cgi-bin/hgTables), then create the BED14 file using the following code:

cd ~/Documents/Repos/genomesource 
./ucscToBedDetail.py -a ~/Downloads/8090.gene2accession.txt -g ~/Downloads/8090.gene_info.txt ~/Downloads/O_latipes_refGene.bed.gz ~/Downloads/O_latipes_Jul_2017_refGene.bed

6. Sort, gzip, and tabix the BED14 file

cd ~/Downloads/
sort -k1,1 -k2,2n O_latipes_Jul_2017_refGene.bed | bgzip > O_latipes_Jul_2017_refGene.bed.gz
tabix -0 -s 1 -b 2 -e 3 O_latipes_Jul_2017_refGene.bed.gz

7. Sanity check the .bed and .2bit files - Add the .2bit file as a reference, then drag/drop the .bed file into IGB. Confirm that gene models are present, labeled correctly, and the chromosomes listed are in a logical order. Also check that no error messages are present in the Log.

8. Create annots.xml, add O_latipes_Jul_2017 to contents.txt and .htaccess, and create HEADER.md

cd ~/Documents/Repos/quickload
svn mkdir O_latipes_Jul_2017
svn cp H_vulgaris_Apr_2024/annots.xml O_latipes_Jul_2017
nano O_latipes_Jul_2017/annots.xml
nano contents.txt
nano .htaccess
../genomesource/writeQuickLoadHeaderUCSC.py O_latipes_Jul_2017 > O_latipes_Jul_2017/HEADER.md

I've placed a zipped version of the files created for this quickload in Google Drive for the reviewer to take a look at:

Path: research-big-lorainelab > IGB Project Documentation and Plans > IGB Genomes > O_latipes.zip
Link: https://drive.google.com/drive/folders/1bFRx4PqldxNf400n7Vr9SD_dNeNmtpvk?usp=drive_link

I've edited the header to make it specific to NCBI rather than UCSC, added species.txt and synonyms.txt to the zip file, cut down contents.txt to only include this genome, and edited annots.txt to replace UCSC's "refGene" with NCBI's "refSeq".

Let me know if I've updated all of these files correctly!

Testing:

• I first thought we don't need a species.txt as the released version of IGB has O_latipes in its species.txt. However, there is a mistake in the O_latipes species.txt line in the released version of IGB that will need to be fixed in IGBF-4006. In the meantime, please add the attached species.txt when submitting to the SVN repo.
• I would like to include the name medaka in the HEADER.md as the NCBI page includes the name medaka.

Everything else looks good, data load, sequence loads.

I've added the name "Medaka" to HEADER.md and contents.txt. I've also replaced species.txt in the zip file with the file you attached.

Testing: Everything looks good.

The Oryzias latipes genome has been pushed to the SVN repo.

Ready for final review!

I have deployed the latest copy of quickload repository to:

RENCI hosting - http://igbquickload-main.bioviz.org/quickload/ (primary)
UNC Charlotte hosting - http://igbquickload.org/quickload/ (backup)
To test:

• launch IGB and visit each new genome version (see above)
• visit the subdirectories for each genome (by following the links above) and check that there is text describing the genome and datasets visible in IGB itself
• within IGB Available Data section, click any "linkout" icons and make sure a Web page opens and that it goes to a place that describes the dataset somehow
• check that when the datasets load, they look OK - gene models should be boxes with lines connecting them, for instance, and the track labels should be readable and should make sense ("making sense" is a subjective of course! mainly we're looking for problems that could trip up a user and cause confusion.)

Tested following instructions above. Everything looks good.

Closing ticket.