Help: Permission Denied Problem

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Help: Permission Denied Problem

Lee Eric
Hi,

I installed GBrowse-2/03 in Fedora 12 64 bits by using source codes
mode. And when I have access to this demo database, I encounter 500
internal error. I viewed log messages here's the log contents.

[Mon May 24 16:15:37 2010] [error] [client 172.16.14.1] which: no
inkscape in (/sbin:/usr/sbin:/bin:/usr/bin), referer:
https://172.16.14.1/gbrowse2/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/42f19233c6ad24160485d29c4946eb62.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/8e60addebd0cbc183bfdb7cb5be7ae19.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/92f4db946f59896f1adf8a28bb166e66.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/bea923f5da9c56208eaaaad007ed0538.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/77e4274d581044aace4e8a3907c34b5d.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/ae93df1c6bb5529fd010e7e0bab3fb2b.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/0472dddeed92f9190ede3056450d8b03.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/2437e37fb41ae2adc9fbaa6cdaa2dc8e.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/479c6eae0bd28506f5f9e9516e3902d8.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/31d69be78c59dfa5e97521266dbc5787.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/3d7838749a65462d5acfd0b4ec74c158.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/4cd674ce2b09c8d933196b78f86cc592.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/

So could anyone show me some tips on fixing?

Regards,

Eric

------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Help: Permission Denied Problem

Jayaraman, Pushkala
My first guess is that you haven't set permissions correctly.
1.set universal permissions to /var/www/html/gbrowse2
Also make sure all your databases and the
/etc/gbrowse2/[datasource].conf anf GBrwose.conf have universal
permissions.

This should do the trick...I hope!


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: Lee Eric [mailto:[hidden email]]
Sent: Monday, May 24, 2010 3:18 AM
To: Gbrowse Mailing List
Subject: [Gmod-gbrowse] Help: Permission Denied Problem

Hi,

I installed GBrowse-2/03 in Fedora 12 64 bits by using source codes
mode. And when I have access to this demo database, I encounter 500
internal error. I viewed log messages here's the log contents.

[Mon May 24 16:15:37 2010] [error] [client 172.16.14.1] which: no
inkscape in (/sbin:/usr/sbin:/bin:/usr/bin), referer:
https://172.16.14.1/gbrowse2/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/42f19233c6ad24160485d29c4946eb62.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/8e60addebd0cbc183bfdb7cb5be7ae19.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/92f4db946f59896f1adf8a28bb166e66.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/bea923f5da9c56208eaaaad007ed0538.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/77e4274d581044aace4e8a3907c34b5d.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/ae93df1c6bb5529fd010e7e0bab3fb2b.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/0472dddeed92f9190ede3056450d8b03.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/2437e37fb41ae2adc9fbaa6cdaa2dc8e.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/479c6eae0bd28506f5f9e9516e3902d8.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/31d69be78c59dfa5e97521266dbc5787.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/3d7838749a65462d5acfd0b4ec74c158.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
[Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
denied: access to
/gbrowse2/i/yeast/4cd674ce2b09c8d933196b78f86cc592.png denied,
referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/

So could anyone show me some tips on fixing?

Regards,

Eric

------------------------------------------------------------------------
------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Help: Permission Denied Problem

Wes Barris
In reply to this post by Lee Eric
Lee Eric wrote:
> Hi,
>
> I installed GBrowse-2/03 in Fedora 12 64 bits by using source codes
> mode. And when I have access to this demo database, I encounter 500
> internal error. I viewed log messages here's the log contents.

The error messages in your log file indicate that the images in your
gbrowse cache are not readable by your web server.  Normally, when
building from source the "./Build install" step should set the
proper permissions for you.

You can manually fix this by first determining the user that your
web server is running as.  Often this is "nobody".  Next you need
to locate your gbrowse tmp directory location.  The gbrowse tmp
directory will contain several sub-directories: cache, images, locks,
sessions, and userdata.

Once you have these two pieces of information (the web user and the
tmp location) you can make sure that the owner of the tmp directory
and all of its children is the same as the user your web server is
running as ("nobody").  Also make sure the owner has read and write
permissions.  Use chown -R and chmod -R as appropriate.

> [Mon May 24 16:15:37 2010] [error] [client 172.16.14.1] which: no
> inkscape in (/sbin:/usr/sbin:/bin:/usr/bin), referer:
> https://172.16.14.1/gbrowse2/
> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/42f19233c6ad24160485d29c4946eb62.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/8e60addebd0cbc183bfdb7cb5be7ae19.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/92f4db946f59896f1adf8a28bb166e66.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/bea923f5da9c56208eaaaad007ed0538.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/77e4274d581044aace4e8a3907c34b5d.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/ae93df1c6bb5529fd010e7e0bab3fb2b.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/0472dddeed92f9190ede3056450d8b03.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/2437e37fb41ae2adc9fbaa6cdaa2dc8e.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/479c6eae0bd28506f5f9e9516e3902d8.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/31d69be78c59dfa5e97521266dbc5787.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/3d7838749a65462d5acfd0b4ec74c158.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
> denied: access to
> /gbrowse2/i/yeast/4cd674ce2b09c8d933196b78f86cc592.png denied,
> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>
> So could anyone show me some tips on fixing?
>
> Regards,
>
> Eric
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


--
Wes Barris

------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Help: Permission Denied Problem

Lee Eric
Hi,

I fixed this problem by deleting /var/tmp/gbrowse2 folder. After that
GBrowse will recreate those folders with proper permissions.

Regards,

Eric

On Tue, May 25, 2010 at 8:03 AM, Wes Barris <[hidden email]> wrote:

> Lee Eric wrote:
>>
>> Hi,
>>
>> I installed GBrowse-2/03 in Fedora 12 64 bits by using source codes
>> mode. And when I have access to this demo database, I encounter 500
>> internal error. I viewed log messages here's the log contents.
>
> The error messages in your log file indicate that the images in your
> gbrowse cache are not readable by your web server.  Normally, when
> building from source the "./Build install" step should set the
> proper permissions for you.
>
> You can manually fix this by first determining the user that your
> web server is running as.  Often this is "nobody".  Next you need
> to locate your gbrowse tmp directory location.  The gbrowse tmp
> directory will contain several sub-directories: cache, images, locks,
> sessions, and userdata.
>
> Once you have these two pieces of information (the web user and the
> tmp location) you can make sure that the owner of the tmp directory
> and all of its children is the same as the user your web server is
> running as ("nobody").  Also make sure the owner has read and write
> permissions.  Use chown -R and chmod -R as appropriate.
>
>> [Mon May 24 16:15:37 2010] [error] [client 172.16.14.1] which: no
>> inkscape in (/sbin:/usr/sbin:/bin:/usr/bin), referer:
>> https://172.16.14.1/gbrowse2/
>> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/42f19233c6ad24160485d29c4946eb62.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/8e60addebd0cbc183bfdb7cb5be7ae19.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/92f4db946f59896f1adf8a28bb166e66.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/bea923f5da9c56208eaaaad007ed0538.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/77e4274d581044aace4e8a3907c34b5d.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:38 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/ae93df1c6bb5529fd010e7e0bab3fb2b.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/0472dddeed92f9190ede3056450d8b03.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/2437e37fb41ae2adc9fbaa6cdaa2dc8e.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/479c6eae0bd28506f5f9e9516e3902d8.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/31d69be78c59dfa5e97521266dbc5787.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/3d7838749a65462d5acfd0b4ec74c158.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>> [Mon May 24 16:15:41 2010] [error] [client 172.16.14.1] (13)Permission
>> denied: access to
>> /gbrowse2/i/yeast/4cd674ce2b09c8d933196b78f86cc592.png denied,
>> referer: https://172.16.14.1/cgi-bin/gb2/gbrowse/yeast/
>>
>> So could anyone show me some tips on fixing?
>>
>> Regards,
>>
>> Eric
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
> --
> Wes Barris
>

------------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse