Gbrowse install errors

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Gbrowse install errors

xiongjie

Hi, all


I have install the lastest gbrowse in REDHAT 7. Now I can visit the YEAST test page, but there  seems many problem:

 

First, the tmp images can not be shown in the webpage. The /var/tmp/gbrowse2/images directory do not have files wrote. I checked the error log of httpd, seems like bellow:

[Mon Jan 12 15:19:19.904818 2015] [authz_core:error] [pid 49455] [client 10.21.211.40:51181] AH01630: client denied by server configuration: /var/tmp/gbrowse2/images/yeast/

e305da83dbecdd03d4661778eec9bae9.png, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast/?name=chrI

 

 

I also checked the gbrowse.conf in httpd/conf.d/, like this:

<Directory "/var/tmp/gbrowse2/images/">

  Order allow,deny

  Allow from all

</Directory>

 

And the directory in "/var/tmp/gbrowse2/images/"> like :

[jiexiong@path-hpc3 gbrowse2]$ pwd

/var/tmp/gbrowse2

[jiexiong@path-hpc3 gbrowse2]$ ls -al

total 4

drwxrwxrwx.  3 apache apache   19 Jan 12 15:16 .

drwxrwxrwx. 20 root   root   4096 Jan 12 14:22 ..

drwxrwxrwx.  2 apache apache    6 Jan 12 15:18 images

[jiexiong@path-hpc3 gbrowse2]$

 

 

File in “/var/www/html/gbrowse2” :

[jiexiong@path-hpc3 gbrowse2]$ pwd

/var/www/html/gbrowse2

[jiexiong@path-hpc3 gbrowse2]$ l

total 192K

-rwxrwxrwx. 1 root   root 3.1K Jan 12 13:50 vbox_index.html

-rwxrwxrwx. 1 root   root 4.5K Jan 12 13:50 index.html

-rwxrwxrwx. 1 root   root 5.2K Jan 12 13:50 gmod_cog.jpeg

-rwxrwxrwx. 1 root   root 7.7K Jan 12 13:50 general_help.html.zh

-rwxrwxrwx. 1 root   root  20K Jan 12 13:50 general_help.html

-rwxrwxrwx. 1 root   root 4.6K Jan 12 13:50 gbrowse_syn_help.html

-rwxrwxrwx. 1 root   root  69K Jan 12 13:50 gbrowse_karyotype_help.html

-rwxrwxrwx. 1 root   root 2.9K Jan 12 13:50 cloud_index.html

-rwxrwxrwx. 1 root   root  42K Jan 12 13:50 annotation_help.html

drwxrwxrwx. 7 root   root   77 Jan 12 13:50 images

drwxrwxrwx. 3 root   root 4.0K Jan 12 13:50 css

drwxrwxrwx. 2 root   root 4.0K Jan 12 13:50 example_scripts

drwxrwxrwx. 2 root   root 4.0K Jan 12 13:50 js

drwxrwxrwx. 7 root   root 4.0K Jan 12 13:50 tutorial

lrwxrwxrwx. 1 apache root   24 Jan 12 15:05 i -> /var/tmp/gbrowse2/images

[jiexiong@path-hpc3 gbrowse2]$

 

how can I fix this problem? And it seems that my yeast database do not work correctly, none of the click or drag options works. See attached fig.

 

 

Thanks

 

Jie


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Fwd: Gbrowse install errors

xiongjie



Hi, all


I have install the lastest gbrowse in REDHAT 7. Now I can visit the YEAST test page, but there  seems many problems:

 

First, the tmp images can not be shown in the webpage. The /var/tmp/gbrowse2/images directory do not have files wrote. I checked the error log of httpd, seems like bellow:

[Mon Jan 12 15:19:19.904818 2015] [authz_core:error] [pid 49455] [client 10.21.211.40:51181] AH01630: client denied by server configuration: /var/tmp/gbrowse2/images/yeast/

e305da83dbecdd03d4661778eec9bae9.png, referer: http://172.20.26.72/cgi-bin/gb2/gbrowse/yeast/?name=chrI

 

 

I also checked the gbrowse.conf in httpd/conf.d/, like this:

<Directory "/var/tmp/gbrowse2/images/">

  Order allow,deny

  Allow from all

</Directory>

 

And the directory in "/var/tmp/gbrowse2/images/"> like :

[jiexiong@path-hpc3 gbrowse2]$ pwd

/var/tmp/gbrowse2

[jiexiong@path-hpc3 gbrowse2]$ ls -al

total 4

drwxrwxrwx.  3 apache apache   19 Jan 12 15:16 .

drwxrwxrwx. 20 root   root   4096 Jan 12 14:22 ..

drwxrwxrwx.  2 apache apache    6 Jan 12 15:18 images

[jiexiong@path-hpc3 gbrowse2]$

 

 

File in “/var/www/html/gbrowse2” :

[jiexiong@path-hpc3 gbrowse2]$ pwd

/var/www/html/gbrowse2

[jiexiong@path-hpc3 gbrowse2]$ l

total 192K

-rwxrwxrwx. 1 root   root 3.1K Jan 12 13:50 vbox_index.html

-rwxrwxrwx. 1 root   root 4.5K Jan 12 13:50 index.html

-rwxrwxrwx. 1 root   root 5.2K Jan 12 13:50 gmod_cog.jpeg

-rwxrwxrwx. 1 root   root 7.7K Jan 12 13:50 general_help.html.zh

-rwxrwxrwx. 1 root   root  20K Jan 12 13:50 general_help.html

-rwxrwxrwx. 1 root   root 4.6K Jan 12 13:50 gbrowse_syn_help.html

-rwxrwxrwx. 1 root   root  69K Jan 12 13:50 gbrowse_karyotype_help.html

-rwxrwxrwx. 1 root   root 2.9K Jan 12 13:50 cloud_index.html

-rwxrwxrwx. 1 root   root  42K Jan 12 13:50 annotation_help.html

drwxrwxrwx. 7 root   root   77 Jan 12 13:50 images

drwxrwxrwx. 3 root   root 4.0K Jan 12 13:50 css

drwxrwxrwx. 2 root   root 4.0K Jan 12 13:50 example_scripts

drwxrwxrwx. 2 root   root 4.0K Jan 12 13:50 js

drwxrwxrwx. 7 root   root 4.0K Jan 12 13:50 tutorial

lrwxrwxrwx. 1 apache root   24 Jan 12 15:05 i -> /var/tmp/gbrowse2/images

[jiexiong@path-hpc3 gbrowse2]$

 

how can I fix this problem? And it seems that my yeast database do not work correctly, none of the click or drag options works. See attached fig.

 

 

Thanks

 

Jie



------------------------------------------------------------------------------
New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse