Re: Gbrowse_syn: error pn display page - Overview Scale

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Re: Gbrowse_syn: error pn display page - Overview Scale

Jayaraman, Pushkala
Thanks again Sheldon,
Yes, that was the problem.. and we just worked a hack around it by creating sym links between the document roots and the /tmp folder
It did solve our problem..
:)
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Wednesday, June 09, 2010 2:44 PM
To: Jayaraman, Pushkala
Subject: Re: Gbrowse_syn: error pn display page - Overview Scale

Hi Pushkala,

I think the issue is that gbrowse_syn is using the full URL (with the
server name) for the cached overview image but is not capturing the
fact that you are not using port 80, the default port.  I commited a
patch to svn that uses the url relative to the document root, as other
cached images do.  Please let me know if this solves you problem.

Sheldon


Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Tue, Jun 8, 2010 at 10:49 AM, Jayaraman, Pushkala <[hidden email]> wrote:

> 1.       HTML
>
> In FireFox:
>
> <span id="Overview Scale_image" name="overview" style="background:
> url(&quot;http://hastings.hmgc.mcw.edu//tmp/gbrowse2/oryza/panel_cache/9e/9e238375e3625d26113c4bf687db7502/image.png&quot;)
> no-repeat scroll left top transparent; width: 47px; height: 16px; display:
> block; cursor: text;"></span>
>
>
>
> <div id="overviewselectBox" style="position: absolute; visibility: hidden;
> top: 253.433px; left: 0px; z-index: 100; border: 1px solid black;"></div>
>
>
>
>
>
>
>
> IN Chrome:
>
> <div class="track" id="overview"><div align="center">  <map
> name="overview_map"><area shape="rect" coords="25,18,61,51" alt="recenter"
> href="?ref=3;start=227785;stop=627784;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="61,18,97,51" alt="recenter"
> href="?ref=3;start=1083357;stop=1483356;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="97,18,133,51" alt="recenter"
> href="?ref=3;start=1938929;stop=2338928;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="133,18,169,51" alt="recenter"
> href="?ref=3;start=2794500;stop=3194499;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="169,18,205,51" alt="recenter"
> href="?ref=3;start=3650072;stop=4050071;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="205,18,241,51" alt="recenter"
> href="?ref=3;start=4505643;stop=4905642;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="241,18,277,51" alt="recenter"
> href="?ref=3;start=5361215;stop=5761214;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="277,18,313,51" alt="recenter"
> href="?ref=3;start=6216787;stop=6616786;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="313,18,349,51" alt="recenter"
> href="?ref=3;start=7072358;stop=7472357;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="349,18,385,51" alt="recenter"
> href="?ref=3;start=7927930;stop=8327929;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="385,18,421,51" alt="recenter"
> href="?ref=3;start=8783501;stop=9183500;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="421,18,457,51" alt="recenter"
> href="?ref=3;start=9639073;stop=10039072;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="457,18,493,51" alt="recenter"
> href="?ref=3;start=10494645;stop=10894644;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="493,18,529,51" alt="recenter"
> href="?ref=3;start=11350216;stop=11750215;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="529,18,565,51" alt="recenter"
> href="?ref=3;start=12205788;stop=12605787;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="565,18,601,51" alt="recenter"
> href="?ref=3;start=13061359;stop=13461358;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="601,18,637,51" alt="recenter"
> href="?ref=3;start=13916931;stop=14316930;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="637,18,673,51" alt="recenter"
> href="?ref=3;start=14772503;stop=15172502;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="673,18,709,51" alt="recenter"
> href="?ref=3;start=15628074;stop=16028073;search_src=wild_rice"
> title="recenter">
>
> <area shape="rect" coords="709,18,745,51" alt="recenter"
> href="?ref=3;start=16483646;stop=16883645;search_src=wild_rice"
> title="recenter">
>
> </map><span id="Overview Scale_image" name="overview"
> style="background-image:
> url(http://hastings.hmgc.mcw.edu//tmp/gbrowse2/oryza/panel_cache/4a/4ab6667cf46300e7a2b02d03b259b0ea/image.png);
> background-attachment: initial; background-origin: initial; background-clip:
> initial; background-color: initial; width: 770px; height: 54px; display:
> block; cursor: text; background-position: 0% 0%; background-repeat:
> no-repeat no-repeat; "></span></div></div>
>
> <div id="overviewselectBox" style="position: absolute; visibility: hidden;
> top: 256px; left: 0px; z-index: 100; border-top-width: 1px;
> border-right-width: 1px; border-bottom-width: 1px; border-left-width: 1px;
> border-top-style: solid; border-right-style: solid; border-bottom-style:
> solid; border-left-style: solid; border-top-color: black;
> border-right-color: black; border-bottom-color: black; border-left-color:
> black; "></div>
>
>
>
>
>
> I see that the Overview Scale Image highlights the place which ought to have
> the scale.. and the overviewselectBox does not appear..
>
> I have attached my conf files and also the "htdocs" folder which has the
> images, css, js and tutorial folders..
>
>
>
> 2.       Script:
>
> I also see it breaking on
>
> Balloon.prototype.setActiveCoordinates = function(evt) Line 764 of
> balloon.js -- a DHTML library for balloon tooltips
>
>
>
> 3.       IMAGE:
>
> http://hastings.hmgc.mcw.edu//tmp/gbrowse2/oryza/panel_cache/4a/4ab6667cf46300e7a2b02d03b259b0ea/image.png
>
> This gives me a 404 not found.
>
>
>
> 4.       JS Console on Chrome:
>
> I get Resource interpreted as image but transferred with MIME type
> text/html. Image.png
>
>
>
>
>
>
>
>
>
> Here is the Directory Path:
>
> For future reference, here is where you've installed GBrowse's various
> components:
>
> GBrowse documentation, stylesheets and in-memory databases.
>
> /usr/local/gbrowse2/htdocs
>
> GBrowse configuration files
>
> /usr/local/gbrowse2/etc/GBrowse.conf
>
> Preinstalled sample database(s)
>
> /usr/local/gbrowse2/databases
>
> Online tutorial and sample data files
>
> /usr/local/gbrowse2/htdocs/tutorial.
>
> GBrowse CGI (web) scripts
>
> ·         /usr/local/apache3/cgi-bin/gbrowse
>
> ·         /usr/local/apache3/cgi-bin/gbrowse_img
>
> ·         /usr/local/apache3/cgi-bin/gbrowse_details
>
> Installation and configuration manual
>
> GBrowse 2.0 HOWTO
>
> Temporary directories for cached images and sessions.
>
> /usr/local/gbrowse2/tmp
>
>
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
>

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