Re: [Gmod-ajax] jBrowse set up issue

[Yang, Chin-R. (NIH/N. [E] <chi...@ni...>]

Hi Scott,

Thank you for your prompt reply.

Yes, my plan is to setup a web server for others to access my data in the future.
I was thinking to test it out in a local machine first.

The error message I found from the Chrome browser is
“Failed to load resource: the server responded with a status main.bundle.js:1 of 404 (Not Found)”

Thank you very much for your advice.
I will talk to our IT people to see how to get an access for a web server as well.


Chin-Rang


From: Scott Cain <sc...@sc...>
Sent: Tuesday, August 13, 2019 1:46 PM
To: Yang, Chin-Rang (NIH/NHLBI) [E] <chi...@ni...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] jBrowse set up issue

Hi Chin-Rang,

I have a few suggestions: First, if you are only looking to display your RNASeq reads locally, you'll probably find it a lot easier to use the JBrowse desktop application: https://jbrowse.org/docs/jbrowse_desktop.html (download at http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html).  It's JBrowse running in an Electron wrapper, so you don't have to deal with a webserver at all.

On the other hand if your goal is to get a server running so you can share it with lab mates or the like, you can continue down the road using a webserver.  I have no experience trying to set up JBrowse on a Windows machine.  While the webserver part should work fine, I would guess that you're likely to run into problems running the processing perl scripts like prepare-refseqs.pl<http://prepare-refseqs.pl> and flatfile-to-json.pl<http://flatfile-to-json.pl>, but that's a step or two away at the moment.  To address your immediate problem, please open your javascript console to see if there are any errors that might help us figure out what's going on.

Good luck,
Scott


On Tue, Aug 13, 2019 at 10:07 AM Yang, Chin-Rang (NIH/NHLBI) [E] via Gmod-ajax <gmo...@li...<mailto:gmo...@li...>> wrote:
Hi,

I am trying to setup jBrowse on a Apache server at the local Windows 10 workstation to display my RNA-Seq data.

The Apache server is running OK. Test web page shows “It works”.

I put the Jbrowse folder in the Apache htdocs folder.

When I run
http://localhost/jbrowse/
the web page shows “ Loading …”

I tried the “volvox” example, get tracks.conf, volvox.fa, volvox.fa.fai in the data folder.
Then run
http://localhost/jbrowse/?data=data
the web page shows “Loading …”, but nothing loaded …

I am wondering if other people have the similar issue.
Do I need to set jbrowse up in a really working web server, not a local one?

Please advise. Thank you.

Chin-Rang

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research