Soft links for the "uri" value

[tao-bioinfo]

I set up a jbrowse instance and the "volvox" test data runs well. Then I make the following modifications to replace volvox.2bit with a soft link:

cd test_data/volvox
mv volvox.2bit /some/path/
ln -s /some/path/volvox.2bit volvox.2bit

Then JBrowse failed to launch as it complaints no volvox.2bit file. When I replace volvox.2bit with the original file, the session became normal again.

Since my real genome file is very large, I hope to put it in other directories outside the JBrowse path. Possible to do that?

[cmdcolin]

This should actually be fine to do this. What server are you using? Maybe the server cannot traverse symlinks?

[tao-bioinfo]

I use npx introduced in https://jbrowse.org/jb2/docs/quickstart_web

[cmdcolin]

It seems like probably the serve package server (npx serve runs the npm serve package https://www.npmjs.com/package/serve) does not support symlinks by default. It requires a custom configuration e.g. like this https://github.com/vercel/serve-handler#options

If you use a different server like apache or nginx then you will have normal symlink support out of the box. I'd probably just use the serve package for quick testing and switch to a normal web server if possible and then you can use symlinks

[tao-bioinfo]

Thank you for your suggestion. However I can't find a tutorial on how to use apache for JBrowse 2 in https://jbrowse.org/jb2/docs/.

Besides, I've noticed that some features in JBrowse 1 haven't been imported in JBrowse 2 yet. (Such as Name Searching #1484) which is very important to me. I've turned to JBrowse 1 temporarily.

I hope to list the features that exist in JBrowse 1 but haven't yet been implemented in JBrowse 2 in https://jbrowse.org/jb2/features#feature-comparison-of-jbrowse-2-vs-jbrowse-1 .

[cmdcolin]

Thanks, I started a couple things here #1581. It's true that there are some missing features in jbrowse 2

We will try to get those things added as soon as possible:)

[rbuels]

Yes, JB2 can point to data at any URL. In fact, I think it's best (though there are diverse opinions on this within the JB2 development team) to keep your data outside of the JB2 directory and just use absolute URIs in the configuration to point your JB2 at it.

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On Mon, Dec 21, 2020 at 5:09 PM billzt ***@***.***> wrote: I set up a jbrowse instance and the "volvox" test data runs well. Then I make the following modifications to replace volvox.2bit with a soft link: cd test_data/volvox mv volvox.2bit /some/path/ ln -s /some/path/volvox.2bit volvox.2bit Then JBrowse failed to launch as it complaints no volvox.2bit file. When I replace volvox.2bit with the original file, the session became normal again. Since my real genome file is very large, I hope to put it in other directories outside the JBrowse path. Possible to do that? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1580>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAASAFPB4GAWGYLIMUIU34TSV7WS3ANCNFSM4VE6FGZQ> .

[tao-bioinfo]

OK. But how can I use powerful http servers such as apache for JB2? I can't find documents in https://jbrowse.org/jb2/docs/

[cmdcolin]

@billzt the basic idea is that jbrowse 2 (like jbrowse 1) is "static site compatible" meaning that you can unzip the release for jbrowse 2 into /var/www/html/jbrowse2/ folder for example, and then visit http://localhost/jbrowse2/

.... could use a little better documentation though

[tao-bioinfo]

OK. So easy? I was mislead by this description in https://jbrowse.org/jb2/docs/quickstart_web:

JBrowse 2 requires a web server to run. It won't work if you try to directly open the index.html in your web browser.

Then I had thought it was speicial like a Flask app or ruby app that needs special configuration to Apache.

[cmdcolin]

Ah, thanks for pointing out this sentence as being potentially confusing. That sentence about "directly opening the index.html" was referring to double-clicking the index.html and opening up the file:/// URL version...we will try to clarfiy that.

JBrowse 2 is very much the same style as JBrowse 1 and so it should work with your existing style of JBrowse 1 server setup