Translation of JBrowse1 REST API to JBrowse2

[Michael Thang]

Hi Apollo Team,

I would like to find out how to translate this Jbrowse1 trackList.json to Jbrowse2. I just borrowed the trackList.json online, but I am running into the same situation where I have my Jbrowse1 configured to run API. I am exploring the posssiblity to use the same trackList.json format for Jbrowse2. However, the Jbrowse2 is using config.json instead and the json looks different. Therefore, I dont know if all these options are still applicable for Jbrowse2.

[Nathan Dunn]

On Oct 11, 2023, at 11:40 PM, Michael Thang <m.t...@qfab.org> wrote:

Hi Apollo Team,

I would like to find out how to translate this Jbrowse1 trackList.json to Jbrowse2. I just borrowed the trackList.json online, but I am running into the same situation where I have my Jbrowse1 configured to run API. I am exploring the posssiblity to use the same trackList.json format for Jbrowse2. However, the Jbrowse2 is using config.json instead and the json looks different. Therefore, I dont know if all these options are still applicable for Jbrowse2.

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[Colin]

Hi Michael,

Many of the JBrowse 1 options do not automatically apply to JBrowse 2 because the config.json format is quite a bit different from trackList.json.

I also see that your trackList.json refers to a "REST" data adapter from JBrowse 1 (JBrowse/Store/SeqFeature/REST) but this data adapter type was not added to JBrowse 2. We did not add this to JBrowse 2 because it is hard or awkward to design a "blessed"  or "recommended" REST API format that we want users to implement.  If you do want to make an adapter for your REST API, you can write a custom plugin to do so. I may be biased because I wrote a lot of data adapters for various REST APIs on the web as plugins (mygene.info adapter, UCSC rest api adapter, etc) but my feeling is that it  is relatively little code (100-200 lines for example) and it can actually be useful, as a developer, to be in control of the client code that is accessing your particular REST API.

If your main concerns are getting a JBrowse 1 REST API working with JBrowse 2 I can elaborate, or I can help with any of the other JBrowse 2 upgrade steps too :)

-Colin

[Michael Thang]

Hi Colin,

Thank you for speedy reply and clarification ! I can relate the REST API (aka mygene.info) to a project I am working on and using this Django framework to embed jbrowse into it (machado). I am keen to use Jbrowse2 but the main issue is how to translate the trackList.json to config.json for my project. As you mentioned above, most of the Jbrowse1 options are dropped for Jbrowse2. I guess I need to investigate a bit more to see how much work I need to use Jbrowse2 for my project. The good news is the Machado Framework does come with API setup and I am trying to understand how to combine the API and the Jbrowse2 in the config.json (Jbrowse2) based on the trackList.json (Jbrowse1) format.

I think this is the config.json you use to retrieve reference genome and tracks using API call. For me, it is a bit difficult to understand the options you use in the config.json. I believe there must be a documentation somewhere . can you please point me to the documentation if available? 

To date, I managed to setup the Jbrowse2 running on my apache server without any problems. What I want to explore next is to work on the REST API call to query and show the tracks/assemblies of interest on an embedded Jbrowse2. However, I am kind of stuck at the moment.

Best

[Colin]

Hi Michael

Sorry for delay in reply, definitely feel free to let us know if you have any updates or questions. Regarding docs, main portal is here https://jbrowse.org/jb2/docs

Developer docs related to things like plugins are here, for example, creating an adapter which can be used for adapting to a REST APIs https://jbrowse.org/jb2/docs/developer_guides/creating_adapter/ and then our embedded components that you refer to have links to 'storybook demos' and other docs here https://jbrowse.org/jb2/docs/embedded_components/

If you are accustomed to JBrowse 1 terminology, here is a rough mapping

JBrowse 1->JBrowse 2

storeClass->adapter (there is no more urlTemplate, you look at the config docs https://jbrowse.org/jb2/docs/config_guides/alignments_track/ or "auto-generated config docs" for each little schema type https://jbrowse.org/jb2/docs/config/bamadapter/ and you will see that there is instead things like bamLocation, gffGzLocation, etc. sort of different for each track type)

trackList->track label->config.json track trackId

trackList track key->config.json track name

bin/prepare-refseqs.pl->jbrowse add-assembly (assemblies have a special area of the config that provides a ReferenceSequenceTrack)

bin/flatfile-to-json.pl->jbrowse add-track

For custom sequence fetching and feature fetching, may require hand-editing the config.json. The config.json you linked uses the "biothings" plugin to fetch from mygene.info and myvariant.info. Example code for that here https://github.com/cmdcolin/jbrowse-plugin-biothings-api/blob/master/src/MyGeneAdapter.ts. Can add more info about plugins if interested

-Colin