Re: [Gmod-ajax] how to use jbrowse2 in a server environment?

[Colin <col...@gm...>]

Hi Peter
This is a good question, probably there are many ways to approach this
depending on your wants/needs

JBrowse 2 itself is sort of 'lightweight' on server resources because it
doesn't actually run code server side. JBrowse 2 is just
javascript/css/html that is run on a users client side browser. That means,
you can create "multiple jbrowse 2 instances" on your server and you don't
have to worry about any conflicts

For example

cd /var/www/html/
jbrowse create instance1
jbrowse create instance2
jbrowse add-assembly organism1.fa --out instance1 --load copy
jbrowse add-assembly organism1.fa --out instance2 --load copy

That will create /var/www/html/instance1 and /var/www/html/instance2, that
can be visited via http://yourhost/instance1 and http://yourhost/instance2,
each separate jbrowse 2 instances. You could add .htaccess to the instance1
folder and instance2 folder for different access levels, that would add
'simple http authentication'. Little old school, but works :)


At one point I wanted to create a demo of this but just wasn't sure how
best to distribute it (e.g. could create a docker image or just a simple
FAQ entry documenting the above steps)


Also note: we have some interesting workflows inside jbrowse 2 that help
access authenticated resources from third party websites. This is
*generally* used when accessing a third party domain e.g. your jbrowse is
on http://yoursite.com/jbrowse2 but you want to access resources on
http://someothersite.com/resource. In this case, jbrowse 2 has
functionality called "internet accounts" that can access those third party
resources via a number of built in ways, or can be extended to do custom
stuff if you write plugins. This is likely not something you would need to
implement if you are in control of your distribution, but could be an
option. This workflow could also allow there to be a single jbrowse2 folder
and then you have multiple config files in that folder that have different
access levels, but this may be more complicated than the above

Also also note: if you are using some sort of framework, and it accepts
e.g. react components on certain authenticated routes, you can consider
using our embedded components like @jbrowse/react-linear-genome-view. That
may be a little more "modern" by some interpretations. We are soon
releasing the entire "jbrowse web app" as a react component that can be
installed via NPM (currently only e.g. the linear genome view is on NPM,
but the full "jbrowse web app" react component will be on NPM pretty soon)

-Colin

On Wed, Jun 7, 2023 at 11:35 AM Peter Minogue via Gmod-ajax <
gmo...@li...> wrote:

> To the JBrowse 2 team,
>
>
>
> I was looking at this next-generation genome browser in a Linux server
> environment. The idea is , have it installed ‘centrally’ on a Linux server
> and then display it via a browser or so on one’s local machine. This would
> avoid having to set this up for multiple people. This would require some
> sort of user authentication I presume on the web application, but I can’t
> see any mention of it in the documentation. I presume it would just use the
> Linux authentication subsystem to do this? How does one do this?
>
>
>
> Considering more people will be doing complete genomes at RSB this kind of
> setup will become more popular. It is the easiest way to share the assembly
> and annotation + else within a group using all the users and group file
> permissions on the central Linux server.
>
>
>
> Is this possible? Any documentation on doing this? Or is it single
> user/workstation only application?
>
>
>
>
>
> Cheers
>
> Peter
>
>
>
> ---------------------------------------------------------------
>
> Peter Minogue
>
> IT Infrastructure
>
> Information Technology Services
>
> Research School of Biology
>
> ANU College of Science, Robertson Bld 46
>
> The Australian National University
>
> Canberra ACT 2600
>
>
>
> RSB Service Desk: hel...@an...
>
> M 0423 136 495
>
> http://biology.anu.edu.au/people/peter-minogue
>
> The RSB IT Infrastructure User Documentation is here
> <https://infrawiki.rsb.anu.edu.au/doku.php?id=rsb_it:infrastructure:userdoco:start>
>
> *the Queen said “other capital cities may claim to be centres of transport
> *
>
> *or commerce or military strongholds, but let Canberra's pride be
> scholarship.”*
>
>
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