Unassigning since SK will be out of town during the sprint.

I have a doubt in this. Are these the files being referred to here:
Galaxy : https://github.com/galaxyproject/galaxy/blob/dev/tool-data/shared/ucsc/builds.txt.sample
IGB synonyms.txt : http://www.igbquickload.org/quickload/synonyms.txt
and could you please elaborate on the purpose of http://igbquickload.org/quickload/contents.txt
Thank you.

Prof. [~aloraine], the Galaxy team has provided some links for reference. Could you please take a look at it and let me know if this is what we need?
1) https://usegalaxy.org/api/genomes - They said that as every Galaxy is different, this list applies to so called Galaxy Main, Galaxy EU would have a (more or less) different list
2) http://datacache.galaxyproject.org/ - They have a trove of genome refs that they share across some of the Galaxies that is usually available here

I would like to increase the scope to include Galaxy EU, since we also have a lot of users coming from Germany (mainly) and some other European countries. Can we do this as well?

I'll ask them for that too. I think we should be able to.

Prof. [~aloraine]
They said that every Galaxy has that path.
https://usegalaxy.eu/api/genomes
And the second link has 2 links which lead to reference data. We do have a list of dbkeys there, I checked. So we should be good I think. Could you please check too?

The REST endpoint looks much easier to parse and build into a workflow.

My question:

Where do we find the "dbkey" in the text returned by the REST endpoint?

For example, here is one item in the text being returned from https://usegalaxy.org/api/genomes:

["Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) (Arabidopsis_thaliana_TAIR10)", "Arabidopsis_thaliana_TAIR10"]

There are two items here. The second item looks like it is the dbkey. Is that correct?

It would be great if this endpoint tells us exactly which genome versions are supported by a Galaxy instances.
We can't support every Galaxy in the world, but I bet that if we make sure IGB recognizes every genome version reported by usegalaxy.org (Galaxy main), usegalaxy.eu (European Galaxy), and usegalaxy.au (Australian Galaxy), then we will probably cover all the major Galaxy user groups.

Regarding this pair of strings served from https://usegalaxy.org/api/genomes:

["Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) (Arabidopsis_thaliana_TAIR10)", "Arabidopsis_thaliana_TAIR10"]

It looks like the first string is the human-friendly string (i.e., "display name") that appears in Galaxy UI menus where a user can associate a genome version with a file. The second version looks like it could be the dbkey.

For each, it would be super great if we can get:

• list of chromosome names and their sizes (in base pairs)
• genus name
• species name
• variety or cultivar (only if relevant or required to avoid name collisions)
• month and year of release

If we have this information, then we can build everything we need to show a Galaxy file in IGB, for each genome version supported in the three Galaxies.

Prof. [~aloraine]
The second string in the list is the dbkey. So, for ["Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) (Arabidopsis_thaliana_TAIR10)", "Arabidopsis_thaliana_TAIR10"], "Arabidopsis_thaliana_TAIR10" is the dbkey.

Also, if we hit /api/genomes/<dbkey>, we get the chromosome information from there (name and size). I am currently comparing some samples to verify (Like hg38). Can you please check and verify if this is the information for chromosome names and sizes?

This looks right.

However, I have a question about Arabidopsis_thaliana_TAIR10.

The output from this endpoint - https://usegalaxy.org/api/genomes/Arabidopsis_thaliana_TAIR10 - reports chromosome names as "chr1", "chr2", etc with lower-case "c".

The IGB Quickload site many years ago also used lower-case "c". But I changed us to using upper-case "C" when I realized that The Arabidopsis Information Resource and the entire Arabidopsis community was using upper-case "C". I'm not sure where Galaxy got Arabidopsis_thaliana_TAIR10 from, but they might have got it from me. If they got it from me, then they maybe used the lower-case "c" because that is what I was using. However, I also have a vague memory of someone at the last Galaxy Community Conference saying something about how Galaxy might be making all chromosome names lower-case by default.

Could you ask them about this?

I also checked a few other plant genomes that I think might be using upper-case letters and they were all lower-case in Galaxy also.

Also, could you find the part of their code base (it's python) that supports this "genomes" endpoint.

(By the way I'm really super-glad it is there!!!)

Yes sure, I will ask them and let you know about the lower-case and I'll try to find the part of their code-base too. Will let you know soon. Thank you Prof. [~aloraine].

dbkey is "?" if a user is working with a custom genome in Galaxy.
Galaxy has a manually defined static map that maps dbkeys.

I have included some updates from Galaxy as part of IGBF-781.

Some notes:
The dbkeys for genomes that are also found in UCSC appear to have the same key names. For example, Takifugu rubripes is fr1 in both Galaxy and UCSC. However, as UCSC does not provide plant genomes through its API, Galaxy uses a somewhat different set of keys. For example, the Galaxy EU key for Solanum lycopersicum is Solanum_lycopersicum_Sol_Genomics_itag2.4.

Since the Galaxy keys are the same as UCSC, I focused on the non UCSC genomes that are available in IGB. This list is mostly plant genomes, as many of the non-plant genomes in IGB are provided by UCSC. While the Galaxy main API does not include many plant genomes, the Galaxy EU API does include many plant genomes. This news article discusses the newly added plant genomes and where the data came from.

I manually added as many of the Galaxy EU keys to synonyms.txt as I could identify.

I have created IGBF-2862 regarding an edge case I found while testing loading Galaxy data in IGB.