about the display of Gbrowse2

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about the display of Gbrowse2

JINGJING JIN-2
Hi all,

I have installed the Gbrowse2 successfully.

Then I add my own database using the mysql.

I just change the folder of the database from /var/lib/gbrowse2 to the
/home/chua/db/gbrowse2 after I installed.

Then I also change the configure file like this:

[GENERAL]
config_base            = /etc/gbrowse2   # overridden by environment
variable GBROWSE_CONF
htdocs_base            = /var/www/gbrowse2
url_base               = /gbrowse2
tmp_base               = /tmp/gbrowse2
persistent_base        = /home/chua/db/gbrowse2
userdata_base          = /home/chua/db/gbrowse2/userdata
db_base                = /home/chua/db/gbrowse2/databases

However, the display for the example database –yeast is like the
attachment, it can’t display correctly.

Then, I check the access log, it display like this:
127.0.0.1 - - [25/Oct/2011:22:20:24 -0400] "GET
/gbrowse2/i/yeast/e13a73a48262a46a723755ebebae5662.png HTTP/1.1" 404
533 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:24 -0400] "GET
/gbrowse2/i/yeast/c413aa595d8886d90a8473c94676e07b.png HTTP/1.1" 404
534 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:24 -0400] "GET
/gbrowse2/i/yeast/086bd293f26582e8ad04721a2b65daa5.png HTTP/1.1" 404
533 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:24 -0400] "POST
/cgi-bin/gb2/gbrowse/yeast/ HTTP/1.1" 200 2761
"http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11; U;
Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04 (lucid)
Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:24 -0400] "POST
/cgi-bin/gb2/gbrowse/yeast/ HTTP/1.1" 200 54992
"http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11; U;
Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04 (lucid)
Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/5dfe5355e50d339215f0baa359cf70e6.png HTTP/1.1" 404
533 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/d4f6597d86fa2940117a9d687926b99b.png HTTP/1.1" 404
534 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/90252ff24375444e0bfbab7a4e990230.png HTTP/1.1" 404
532 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/91b360ff083dbe9baab6f426c02c3e56.png HTTP/1.1" 404
534 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/24d4c2c2e34eb1b6ba3b7dbd8a06658a.png HTTP/1.1" 404
532 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/20e2788396275360f7c2aa3d0f0e0867.png HTTP/1.1" 404
534 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/364d9fad32bb0735064d318107542f65.png HTTP/1.1" 404
534 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/8661fd84dd1ca3aa0b2ea0ccd4a688d1.png HTTP/1.1" 404
532 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:20:25 -0400] "GET
/gbrowse2/i/yeast/65ce42b5d5d9c23ded630bdd6a85349c.png HTTP/1.1" 404
533 "http://localhost/cgi-bin/gb2/gbrowse/yeast/" "Mozilla/5.0 (X11;
U; Linux x86_64; en-US; rv:1.9.2.23) Gecko/20110921 Ubuntu/10.04
(lucid) Firefox/3.6.23"
127.0.0.1 - - [25/Oct/2011:22:28:39 -0400] "GET /cgi-bin/gb2/gbrowse/arabi


And the error log is like this:
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/www/gbrowse2/css/snapshots.css, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/www/gbrowse2/js/snapshotManager.js, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/www/gbrowse2/js/snapshotManager.js, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:23 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:24 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:24 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:24 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/
[Tue Oct 25 22:20:25 2011] [error] [client 127.0.0.1] File does not
exist: /var/tmp/gbrowse2/images, referer:
http://localhost/cgi-bin/gb2/gbrowse/yeast/

Can anyone give me some suggestions where I am wrong?

Thanks!

jingjing

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Re: about the display of Gbrowse2

JINGJING JIN-2
the display is like this:

http://generic-model-organism-system-database.450254.n5.nabble.com/file/n4938503/Untitled.png 

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View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/about-the-display-of-Gbrowse2-tp4938501p4938503.html
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The demand for IT networking professionals continues to grow, and the
demand for specialized networking skills is growing even more rapidly.
Take a complimentary Learning@Cisco Self-Assessment and learn
about Cisco certifications, training, and career opportunities.
http://p.sf.net/sfu/cisco-dev2dev
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