closing this ticket since investigation is completed. Creating another ticket for POC.
Cc: Dr.Nowlan Freese

Created an example for POC from existing quickload:

• hub.txt:

1. hub IGBQuickLoad
2. shortLabel IGB QUICK LOAD
3. longLabel Generated from IGB QuickLoad
4. genomesFile genomes.txt
5. email myEmail@address

• genomes.txt

1. genome C_papaya_Aug_2010
   C_papaya_Aug_2010 is igb quickload name but we need to assign ucsc genome name. To get ucsc genome name we need to check in synomyns.txt. If it is not in synomyns.txt then we assign same igb quickload name.
2. trackDb C_papaya_Aug_2010/trackDb.txt
3. organism Carica papaya
   (we get the organism from species.txt by checking with C_papaya i.e we split the genome name with "_ " an combine first two words in list with "_ " an dchcek if it is present in species.txt. If it is present we get the first column name as organism name)
4. defaultPos chrI:0-6239266
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/genome.txt>
5. twoBitPath http://igbquickload.org/quickload/C_papaya_Aug_2010/C_papaya_Aug_2010.2bit

we can get directly from annots.xml when reference = true or we can fetch from genome version folder
http://igbquickload.org/quickload/C_papaya_Aug_2010/

1. Organism, defaultPos and 2 bit file are not mandatory
   It is required only when ucsc genome name is not matched with igbquickload name

• trackDb.txt

1. track Caricapapaya
2. bigDataUrl C_papaya_Aug_2010.bed.gz
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/annots.xml> (name)
3. shortLabel Carica papaya gene models from Phytozome v7
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/annots.xml>
4. longLabel protein-coding gene models
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/annots.xml>
5. type bed
6. visibility dense (hard coded)

track hub : https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/trackHub1/hub.txt

The above track hub did not work since i need to convert bigdataurl to bed

Example trackhub repo that uses the same data as the QuickLoad: https://bitbucket.org/nfreese/testquickload/src/main/trackHub/
The raw URL to the trackhub was not working for UCSC, but the API url does seem to work: https://api.bitbucket.org/2.0/repositories/nfreese/testquickload/src/main/trackHub/hub.txt

Note that UCSC does not accept gzipped bed files (see this link for additional details), so I had to change the bed annotation to a bigBed. See IGBF-2978 for details on how to do that.

bedToBigBed -as=bedDetail.as -tab -type=bed12+2 E_unicornis_Jul_2043.bed chrom.sizes E_unicornis_Jul_2043.bb

Note that because this genome is new (not a genome already found in UCSC), some additional fields were required. For example, in the genomes.txt I had to include the organism, defaultPos, and twoBitPath properties in that order.

Test QuickLoad repository: https://bitbucket.org/nfreese/testquickload/src/main/
Test QuickLoad URL for adding to IGB as a QuickLoad: https://bitbucket.org/nfreese/testquickload/raw/main/quickload/
Info about the annots.xml file: https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml

Genome will appear as E_unicornis in the Species dropdown in IGB.

Note: For some reason IGB is throwing an error when trying to load the sequence (2bit) stored in the Downloads folder in Bitbucket. This is not an issue for the gzipped bed file. I have copied the 2bit file to CyVerse and pointed at it in the annots.xml.

Github link : https://github.com/udaya67/ucsc_trackhubs

I followed the instructions in ucsc quick start guide https://genome.ucsc.edu/goldenPath/help/hubQuickStart.html and created the below files locally.

• hub.txt
• genomes.txt
• trackDb.txt

To create hub.txt we need to create below three files in specific order:
myHub/ - directory containing track hub files

• hub.txt - a short description of hub properties
• genomes.txt - list of genome assemblies included in the hub data
• hg19/ - directory of data for the hg19 (GRCh37) human assembly
  • trackDb.txt - display properties for tracks in this directory

There is a option called useOneFile on. Using this command in hub.txt we can have all files in single file but the limitation is that we cannot refer to different genomic assemblies in genomes.txt. It is used for only single genome.

To host the files in server i used the below python command and ran the server in my local. But it did not work due to some restrictions.
python -m http.server 8000

So, I hosted the files in github and generated the url and pasted the url in connected hub. The hub.txt file got added succesfully.
https://udaya67.github.io/ucsc_trackhubs/hub.txt

Now I will start exploring the data in each file.

• Important file: https://bitbucket.org/lorainelab/hub-facade/src/main/igb_trackhub/api/create_resources.py
• UCSC Track hub URL: https://genome.ucsc.edu/cgi-bin/hgHubConnect
• This is the hub.txt API call: https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/000/001/905/GCA_000001905.1/hub.txt
• Documentation for setting up your own track hub: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Setup
• File that is getting the API calls: https://bitbucket.org/lorainelab/hub-facade/src/main/igb_trackhub/api/views.py