Keep some genomes private?

[jhumann]

In JB1 we could keep genomes semi-private because each genome was separate. But with JB2 all genomes are added to the same config file so we can have multiple genomes in one session. Is there currently a way to exclude some loaded genomes so they are hidden? Or a way to have multiple config files that we can use to control which genomes are available to be selected? While most of our genomes are publicly available on our databases, we do occasionally have pre-pub genomes that the contributors want private access to.

[cmdcolin]

there are several options for this, that may meet different levels of requirements/have different levels of effort needed

1. you can make two jbrowse 2 instances, one that is public, the other where the jbrowse2 folder is HTTP basic protected or similar. jbrowse is just a folder of static files so this tends to be fairly easy

2. you can use multiple config.json files similar to your jbrowse 1 solution. jbrowse 2 has a ?config= URL parameter similar to the jbrowse 1 ?data= URL parameter, so you could have a public config.json file and a private config.json file. in this case the private config.json could be security by obscurity, or it could use the internet accounts concept listed below to rigorously protect it

3. you can use the internetAccounts concept. tracks and assemblies in the config.json can have an associated "internet account" that prompts the user for a login. this allows you to have "private data" in your config.json. note that everyone would see these tracks and assemblies though, they are not hidden, but would be prompted for login to access them. we have an example here that shows both oauth and HTTP basic authentication for both tracks and assemblies https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/config_auth.json

4. you can use some other login system that is sort of native to whatever your website uses. my feeling is that most "normal" websites that have logins have a system like this, but (at least as a jbrowse dev not involved in these projects) it seems like people have trouble adapting jbrowse to this model for whatever reason. if you have something like this let me know. there are probably various options including jbrowse "embedded components" on authenticated pages, renaming index.html to index.php in jbrowse-web and adding an auth check, or other such things.

[cmdcolin]

sorry for typos in the above, i typed it out too fast.

also I am sorry I missed talking with you at PAG, if interested feel free to schedule an office hours https://jbrowse.org/jb2/contact/