Re: [Gmod-ajax] jBrowse set up issue

[Scott C. <sc...@sc...>]

Hi Chin-Rang,

That's good news--the only downside to using the non-dev version is that
you can't install plugins if there are any you want--but that's a problem
for another day :-)

Scott


On Tue, Aug 13, 2019 at 11:55 AM Yang, Chin-Rang (NIH/NHLBI) [E] <
chi...@ni...> wrote:

> Yes, it is working now with non-dev version.
>
> Thank you very much.
>
>
>
> Chin-Rang
>
>
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Tuesday, August 13, 2019 2:26 PM
> *To:* Yang, Chin-Rang (NIH/NHLBI) [E] <chi...@ni...>
> *Subject:* Re: [Gmod-ajax] jBrowse set up issue
>
>
>
> Hi Chin-Rang,
>
>
>
> The trick with sorting out a 404 error is to examine the url it's trying
> to fetch and then figure out why the file it's looking for isn't where it
> expects.  If you have jbrowse-dev, you'll need to run setup.sh (oh, which
> probably won't work on Windows) to generate the javascript bundle files.  I
> believe if you get the non-dev version, those files are already generated.
>
>
>
> Scott
>
>
>
>
>
> On Tue, Aug 13, 2019 at 11:24 AM Scott Cain <sc...@sc...> wrote:
>
>
>
>
>
> On Tue, Aug 13, 2019 at 11:00 AM Yang, Chin-Rang (NIH/NHLBI) [E] <
> chi...@ni...> wrote:
>
> 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 and 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...> 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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> Gmo...@li...
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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
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


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