Re: grows permission issue for OSX

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Re: grows permission issue for OSX

girlwithglasses
Hello J Fang,

Have you configured Apache (through the httpd.conf file) to allow access to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will install the Perl modules, but you still need to set up Apache.

I've cc'd the GBrowse mailing list; please keep it cc'd in your response as other list members may have advice.

Thanks!


On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen <[hidden email]> wrote:
Hello there,

I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX 10.8.3).  It keeps giving me the following error message when I access the example yeast dataset: 

Forbidden

You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this server.

It gives me the same error even after I chmod /var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2 to 777.

Could you let me know how I can fix the problem.

Thanks very much in advance,
J Fang






--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


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Re: grows permission issue for OSX

Fang, Jianwen
Thanks Amelia.  It works once I revised https.conf.  
Now I am trying to enable fastCGI.  
I follow the procedure described in http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_10.8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get similar 403 error:  You don't have permission to access /fgb2/gbrowse/ on this server.  I guess I have missed some steps.  Could any one give me some advice?

Thanks again,
JF



From: Amelia Ireland <[hidden email]>
Date: Sunday, April 28, 2013 3:17 PM
To: Jianwen Fang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: grows permission issue for OSX

Hello J Fang,

Have you configured Apache (through the httpd.conf file) to allow access to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will install the Perl modules, but you still need to set up Apache.

I've cc'd the GBrowse mailing list; please keep it cc'd in your response as other list members may have advice.

Thanks!


On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen <[hidden email]> wrote:
Hello there,

I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX 10.8.3).  It keeps giving me the following error message when I access the example yeast dataset: 

Forbidden

You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this server.

It gives me the same error even after I chmod /var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2 to 777.

Could you let me know how I can fix the problem.

Thanks very much in advance,
J Fang






--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


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Re: grows permission issue for OSX

Timothy Parnell
Hi,

When you said you modified gbrowse2.conf, are you referring to /etc/apache2/other/gbrowse2.conf ?
This requires that you add extra permissions to allow fastCGI to work as described in my wiki.

A few other questions....

Are you sure you installed FastCGI (OS X 10.8 doesn't include it by default)? You should have the file
/usr/libexec/apache2/mod_fcgid.so
and /etc/apache2/httpd.conf should be updated to include it.

Did you make sure you restart apache? You should see a notice in your /var/log/apache2/error.log referencing mod_fcgid when you restart apache.

Did you try running apachectl configtest to check the syntax?

The instructions I've written mirror what I have on my system. Although it is possible that through upgrades from 10.6 -> 10.7 -> 10.8 there is something lurking in a dark directory in the depths of my system that I have overlooked.

Tim



________________________________
From: Fang, Jianwen [[hidden email]]
Sent: Monday, April 29, 2013 8:46 PM
To: Amelia Ireland
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] grows permission issue for OSX

Thanks Amelia.  It works once I revised https.conf.
Now I am trying to enable fastCGI.
I follow the procedure described in http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_10.8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get similar 403 error:  You don't have permission to access /fgb2/gbrowse/ on this server.  I guess I have missed some steps.  Could any one give me some advice?

Thanks again,
JF



From: Amelia Ireland <[hidden email]<mailto:[hidden email]>>
Date: Sunday, April 28, 2013 3:17 PM
To: Jianwen Fang <[hidden email]<mailto:[hidden email]>>
Cc: "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Subject: Re: grows permission issue for OSX

Hello J Fang,

Have you configured Apache (through the httpd.conf file) to allow access to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will install the Perl modules, but you still need to set up Apache.

I've cc'd the GBrowse mailing list; please keep it cc'd in your response as other list members may have advice.

Thanks!


On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen <[hidden email]<mailto:[hidden email]>> wrote:
Hello there,

I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX 10.8.3).  It keeps giving me the following error message when I access the example yeast dataset:
Forbidden
You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this server.

It gives me the same error even after I chmod /var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2 to 777.

Could you let me know how I can fix the problem.

Thanks very much in advance,
J Fang






--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


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Re: grows permission issue for OSX

Fang, Jianwen
Dear Tim,

Thanks very much for your quick response.  To answer your questions, yes,
I have modified the /etc/apache2/other/gbrowse2.conf to:

<Directory "/Library/Webserver/CGI-Executables/gb2">
 
  Options ExecCGI
  SetEnv GBROWSE_CONF   "/etc/gbrowse2"
  #extra permissions
  Order allow,deny
  Allow from all
</Directory>



Also I can see /usr/libexec/apache2/mod_fcgid.so, which is also included
in /etc/apache2/httpd.conf:

LoadModule fcgid_module libexec/apache2/mod_fcgid.so

I have restarted apache and can see in the error.log:

[Tue Apr 30 12:57:34 2013] [notice] Apache/2.2.22 (Unix) DAV/2
mod_fcgid/2.3.7 mod_ssl/2.2.22 OpenSSL/0.9.8r configured -- resuming
normal operations

I guess factCGI works.

Run "sudo apachectl configtest" return "Syntax OK"

Do you think it has anything to do with setting /gb2 as an alternative to
/cgi-bin/gb2?

http://localhost/cgi-bin/gb2/gbrowse/yeast/ works in my system, but I get
permission issue for the followings:

http://localhost/gb2/gbrowse/yeast
http://localhost/fgb2/gbrowse/yeast

And http://localhost/cgi-bin/fgb2/gbrowse/yeast/ was not found.

If so, could you please let me know how to set the alias?

Thanks again,
JF







On 4/30/13 12:17 PM, "Timothy Parnell" <[hidden email]>
wrote:

>Hi,
>
>When you said you modified gbrowse2.conf, are you referring to
>/etc/apache2/other/gbrowse2.conf ?
>This requires that you add extra permissions to allow fastCGI to work as
>described in my wiki.
>
>A few other questions....
>
>Are you sure you installed FastCGI (OS X 10.8 doesn't include it by
>default)? You should have the file
>/usr/libexec/apache2/mod_fcgid.so
>and /etc/apache2/httpd.conf should be updated to include it.
>
>Did you make sure you restart apache? You should see a notice in your
>/var/log/apache2/error.log referencing mod_fcgid when you restart apache.
>
>Did you try running apachectl configtest to check the syntax?
>
>The instructions I've written mirror what I have on my system. Although
>it is possible that through upgrades from 10.6 -> 10.7 -> 10.8 there is
>something lurking in a dark directory in the depths of my system that I
>have overlooked.
>
>Tim
>
>
>
>________________________________
>From: Fang, Jianwen [[hidden email]]
>Sent: Monday, April 29, 2013 8:46 PM
>To: Amelia Ireland
>Cc: [hidden email]
>Subject: Re: [Gmod-gbrowse] grows permission issue for OSX
>
>Thanks Amelia.  It works once I revised https.conf.
>Now I am trying to enable fastCGI.
>I follow the procedure described in
>http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_10.
>8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get
>similar 403 error:  You don't have permission to access /fgb2/gbrowse/ on
>this server.  I guess I have missed some steps.  Could any one give me
>some advice?
>
>Thanks again,
>JF
>
>
>
>From: Amelia Ireland
><[hidden email]<mailto:[hidden email]>>
>Date: Sunday, April 28, 2013 3:17 PM
>To: Jianwen Fang <[hidden email]<mailto:[hidden email]>>
>Cc:
>"[hidden email]<mailto:[hidden email].
>net>"
><[hidden email]<mailto:[hidden email].
>net>>
>Subject: Re: grows permission issue for OSX
>
>Hello J Fang,
>
>Have you configured Apache (through the httpd.conf file) to allow access
>to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will
>install the Perl modules, but you still need to set up Apache.
>
>I've cc'd the GBrowse mailing list; please keep it cc'd in your response
>as other list members may have advice.
>
>Thanks!
>
>
>On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen
><[hidden email]<mailto:[hidden email]>> wrote:
>Hello there,
>
>I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX
>10.8.3).  It keeps giving me the following error message when I access
>the example yeast dataset:
>Forbidden
>You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this
>server.
>
>It gives me the same error even after I chmod
>/var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2
>to 777.
>
>Could you let me know how I can fix the problem.
>
>Thanks very much in advance,
>J Fang
>
>
>
>
>
>
>--
>Amelia Ireland
>GMOD Community Support
>http://gmod.org || @gmodproject
>
>



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Re: grows permission issue for OSX

Timothy Parnell
Yes, it looks like you have FastCGI installed.
I agree, there's something wrong with the aliases.

Both of these should work, and should indicate the aliases were loaded.
http://localhost/gb2/gbrowse/yeast
http://localhost/fgb2/gbrowse/yeast

The gb2 alias is at the top of the file /etc/apache2/other/gbrowse2.conf.

The fgb2 alias is in the <IfModule mod_fcgid.c> stanza. Here is mine.

<IfModule mod_fcgid.c>
  Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
  <Location /fgb2>
    SetHandler   fcgid-script
  </Location>
  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
  # these directives prevent idle/busy timeouts and may need to be
  # adjusted up or down
  FcgidMinProcessesPerClass 6
  FcgidIOTimeout   3600
  FcgidBusyTimeout 3600
  FcgidMaxRequestLen 2000000000
</IfModule>

If you don't see this, you can try running the following command again in the GBrowse source directory
./Build apache_conf
The output would become the contents of /etc/apache2/other/gbrowse2.conf

Make sure the file is readable by all
sudo chmod -R +r /etc/apache2/other/

Also, make sure at the bottom of /etc/apache2/httpd.conf, you are loading all other confs. You should see
Include /private/etc/apache2/other/*.conf

One other thing. I don't know if this should make a difference or not, but the OS X sets the apache user to be
"_www"  and group "_www". The GBrowse installer assumes "www". This may interfere with some things,
especially when the installer adjusts directory permissions. I have more details in the "Install GBrowse"
section of my guide.
 
________________________________________
From: Fang, Jianwen [[hidden email]]
Sent: Tuesday, April 30, 2013 12:12 PM
To: Timothy Parnell
Cc: [hidden email]
Subject: Re: grows permission issue for OSX

Dear Tim,

Thanks very much for your quick response.  To answer your questions, yes,
I have modified the /etc/apache2/other/gbrowse2.conf to:

<Directory "/Library/Webserver/CGI-Executables/gb2">

  Options ExecCGI
  SetEnv GBROWSE_CONF   "/etc/gbrowse2"
  #extra permissions
  Order allow,deny
  Allow from all
</Directory>



Also I can see /usr/libexec/apache2/mod_fcgid.so, which is also included
in /etc/apache2/httpd.conf:

LoadModule fcgid_module libexec/apache2/mod_fcgid.so

I have restarted apache and can see in the error.log:

[Tue Apr 30 12:57:34 2013] [notice] Apache/2.2.22 (Unix) DAV/2
mod_fcgid/2.3.7 mod_ssl/2.2.22 OpenSSL/0.9.8r configured -- resuming
normal operations

I guess factCGI works.

Run "sudo apachectl configtest" return "Syntax OK"

Do you think it has anything to do with setting /gb2 as an alternative to
/cgi-bin/gb2?

http://localhost/cgi-bin/gb2/gbrowse/yeast/ works in my system, but I get
permission issue for the followings:

http://localhost/gb2/gbrowse/yeast
http://localhost/fgb2/gbrowse/yeast

And http://localhost/cgi-bin/fgb2/gbrowse/yeast/ was not found.

If so, could you please let me know how to set the alias?

Thanks again,
JF







On 4/30/13 12:17 PM, "Timothy Parnell" <[hidden email]>
wrote:

>Hi,
>
>When you said you modified gbrowse2.conf, are you referring to
>/etc/apache2/other/gbrowse2.conf ?
>This requires that you add extra permissions to allow fastCGI to work as
>described in my wiki.
>
>A few other questions....
>
>Are you sure you installed FastCGI (OS X 10.8 doesn't include it by
>default)? You should have the file
>/usr/libexec/apache2/mod_fcgid.so
>and /etc/apache2/httpd.conf should be updated to include it.
>
>Did you make sure you restart apache? You should see a notice in your
>/var/log/apache2/error.log referencing mod_fcgid when you restart apache.
>
>Did you try running apachectl configtest to check the syntax?
>
>The instructions I've written mirror what I have on my system. Although
>it is possible that through upgrades from 10.6 -> 10.7 -> 10.8 there is
>something lurking in a dark directory in the depths of my system that I
>have overlooked.
>
>Tim
>
>
>
>________________________________
>From: Fang, Jianwen [[hidden email]]
>Sent: Monday, April 29, 2013 8:46 PM
>To: Amelia Ireland
>Cc: [hidden email]
>Subject: Re: [Gmod-gbrowse] grows permission issue for OSX
>
>Thanks Amelia.  It works once I revised https.conf.
>Now I am trying to enable fastCGI.
>I follow the procedure described in
>http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_10.
>8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get
>similar 403 error:  You don't have permission to access /fgb2/gbrowse/ on
>this server.  I guess I have missed some steps.  Could any one give me
>some advice?
>
>Thanks again,
>JF
>
>
>
>From: Amelia Ireland
><[hidden email]<mailto:[hidden email]>>
>Date: Sunday, April 28, 2013 3:17 PM
>To: Jianwen Fang <[hidden email]<mailto:[hidden email]>>
>Cc:
>"[hidden email]<mailto:[hidden email].
>net>"
><[hidden email]<mailto:[hidden email].
>net>>
>Subject: Re: grows permission issue for OSX
>
>Hello J Fang,
>
>Have you configured Apache (through the httpd.conf file) to allow access
>to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will
>install the Perl modules, but you still need to set up Apache.
>
>I've cc'd the GBrowse mailing list; please keep it cc'd in your response
>as other list members may have advice.
>
>Thanks!
>
>
>On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen
><[hidden email]<mailto:[hidden email]>> wrote:
>Hello there,
>
>I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX
>10.8.3).  It keeps giving me the following error message when I access
>the example yeast dataset:
>Forbidden
>You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this
>server.
>
>It gives me the same error even after I chmod
>/var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2
>to 777.
>
>Could you let me know how I can fix the problem.
>
>Thanks very much in advance,
>J Fang
>
>
>
>
>
>
>--
>Amelia Ireland
>GMOD Community Support
>http://gmod.org || @gmodproject
>
>



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Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
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Re: grows permission issue for OSX

Fang, Jianwen
I can see in /etc/apache2/other/gbrowse2.conf:

Alias        "/gbrowse2/i/" "/var/tmp/gbrowse2/images/"
Alias        "/gbrowse2"    "/Library/Webserver/Documents/gbrowse2"
ScriptAlias  "/gb2"      "/Library/Webserver/CGI-Executables/gb2"

Also modified the following section to:

<IfModule mod_fcgid.c>
  Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
  <Location /fgb2>
    SetHandler   fcgid-script
  </Location>
  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
  # these directives prevent idle/busy timeouts and may need to be
  # adjusted up or down
  FcgidMinProcessesPerClass 6
  FcgidIOTimeout   3600
  FcgidBusyTimeout 3600
  FcgidMaxRequestLen 2000000000
</IfModule>


I then restarted apache but still get permission error to:
http://localhost/gb2/gbrowse/yeast

But http://localhost/cgi-bin/gb2/gbrowse/yeast/ works just fine.  I guess
it has something to do with alias /gb2 /cgi-bin/gb2.  The fastCGI may work
once this problem is solved.

Thanks again,
JF






On 4/30/13 1:55 PM, "Timothy Parnell" <[hidden email]> wrote:

>Yes, it looks like you have FastCGI installed.
>I agree, there's something wrong with the aliases.
>
>Both of these should work, and should indicate the aliases were loaded.
>http://localhost/gb2/gbrowse/yeast
>http://localhost/fgb2/gbrowse/yeast
>
>The gb2 alias is at the top of the file /etc/apache2/other/gbrowse2.conf.
>
>The fgb2 alias is in the <IfModule mod_fcgid.c> stanza. Here is mine.
>
><IfModule mod_fcgid.c>
>  Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
>  <Location /fgb2>
>    SetHandler   fcgid-script
>  </Location>
>  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>  # these directives prevent idle/busy timeouts and may need to be
>  # adjusted up or down
>  FcgidMinProcessesPerClass 6
>  FcgidIOTimeout   3600
>  FcgidBusyTimeout 3600
>  FcgidMaxRequestLen 2000000000
></IfModule>
>
>If you don't see this, you can try running the following command again in
>the GBrowse source directory
>./Build apache_conf
>The output would become the contents of /etc/apache2/other/gbrowse2.conf
>
>Make sure the file is readable by all
>sudo chmod -R +r /etc/apache2/other/
>
>Also, make sure at the bottom of /etc/apache2/httpd.conf, you are loading
>all other confs. You should see
>Include /private/etc/apache2/other/*.conf
>
>One other thing. I don't know if this should make a difference or not,
>but the OS X sets the apache user to be
>"_www"  and group "_www". The GBrowse installer assumes "www". This may
>interfere with some things,
>especially when the installer adjusts directory permissions. I have more
>details in the "Install GBrowse"
>section of my guide.
>
>________________________________________
>From: Fang, Jianwen [[hidden email]]
>Sent: Tuesday, April 30, 2013 12:12 PM
>To: Timothy Parnell
>Cc: [hidden email]
>Subject: Re: grows permission issue for OSX
>
>Dear Tim,
>
>Thanks very much for your quick response.  To answer your questions, yes,
>I have modified the /etc/apache2/other/gbrowse2.conf to:
>
><Directory "/Library/Webserver/CGI-Executables/gb2">
>
>  Options ExecCGI
>  SetEnv GBROWSE_CONF   "/etc/gbrowse2"
>  #extra permissions
>  Order allow,deny
>  Allow from all
></Directory>
>
>
>
>Also I can see /usr/libexec/apache2/mod_fcgid.so, which is also included
>in /etc/apache2/httpd.conf:
>
>LoadModule fcgid_module libexec/apache2/mod_fcgid.so
>
>I have restarted apache and can see in the error.log:
>
>[Tue Apr 30 12:57:34 2013] [notice] Apache/2.2.22 (Unix) DAV/2
>mod_fcgid/2.3.7 mod_ssl/2.2.22 OpenSSL/0.9.8r configured -- resuming
>normal operations
>
>I guess factCGI works.
>
>Run "sudo apachectl configtest" return "Syntax OK"
>
>Do you think it has anything to do with setting /gb2 as an alternative to
>/cgi-bin/gb2?
>
>http://localhost/cgi-bin/gb2/gbrowse/yeast/ works in my system, but I get
>permission issue for the followings:
>
>http://localhost/gb2/gbrowse/yeast
>http://localhost/fgb2/gbrowse/yeast
>
>And http://localhost/cgi-bin/fgb2/gbrowse/yeast/ was not found.
>
>If so, could you please let me know how to set the alias?
>
>Thanks again,
>JF
>
>
>
>
>
>
>
>On 4/30/13 12:17 PM, "Timothy Parnell" <[hidden email]>
>wrote:
>
>>Hi,
>>
>>When you said you modified gbrowse2.conf, are you referring to
>>/etc/apache2/other/gbrowse2.conf ?
>>This requires that you add extra permissions to allow fastCGI to work as
>>described in my wiki.
>>
>>A few other questions....
>>
>>Are you sure you installed FastCGI (OS X 10.8 doesn't include it by
>>default)? You should have the file
>>/usr/libexec/apache2/mod_fcgid.so
>>and /etc/apache2/httpd.conf should be updated to include it.
>>
>>Did you make sure you restart apache? You should see a notice in your
>>/var/log/apache2/error.log referencing mod_fcgid when you restart apache.
>>
>>Did you try running apachectl configtest to check the syntax?
>>
>>The instructions I've written mirror what I have on my system. Although
>>it is possible that through upgrades from 10.6 -> 10.7 -> 10.8 there is
>>something lurking in a dark directory in the depths of my system that I
>>have overlooked.
>>
>>Tim
>>
>>
>>
>>________________________________
>>From: Fang, Jianwen [[hidden email]]
>>Sent: Monday, April 29, 2013 8:46 PM
>>To: Amelia Ireland
>>Cc: [hidden email]
>>Subject: Re: [Gmod-gbrowse] grows permission issue for OSX
>>
>>Thanks Amelia.  It works once I revised https.conf.
>>Now I am trying to enable fastCGI.
>>I follow the procedure described in
>>http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_10
>>.
>>8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get
>>similar 403 error:  You don't have permission to access /fgb2/gbrowse/ on
>>this server.  I guess I have missed some steps.  Could any one give me
>>some advice?
>>
>>Thanks again,
>>JF
>>
>>
>>
>>From: Amelia Ireland
>><[hidden email]<mailto:[hidden email]>>
>>Date: Sunday, April 28, 2013 3:17 PM
>>To: Jianwen Fang <[hidden email]<mailto:[hidden email]>>
>>Cc:
>>"[hidden email]<mailto:[hidden email]
>>.
>>net>"
>><[hidden email]<mailto:[hidden email]
>>.
>>net>>
>>Subject: Re: grows permission issue for OSX
>>
>>Hello J Fang,
>>
>>Have you configured Apache (through the httpd.conf file) to allow access
>>to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will
>>install the Perl modules, but you still need to set up Apache.
>>
>>I've cc'd the GBrowse mailing list; please keep it cc'd in your response
>>as other list members may have advice.
>>
>>Thanks!
>>
>>
>>On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen
>><[hidden email]<mailto:[hidden email]>> wrote:
>>Hello there,
>>
>>I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX
>>10.8.3).  It keeps giving me the following error message when I access
>>the example yeast dataset:
>>Forbidden
>>You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this
>>server.
>>
>>It gives me the same error even after I chmod
>>/var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2
>>to 777.
>>
>>Could you let me know how I can fix the problem.
>>
>>Thanks very much in advance,
>>J Fang
>>
>>
>>
>>
>>
>>
>>--
>>Amelia Ireland
>>GMOD Community Support
>>http://gmod.org || @gmodproject
>>
>>
>
>
>



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Re: grows permission issue for OSX

Timothy Parnell
Hmmm. that's troubling, as I'm not sure what else to suggest. I haven't had a chance to try the full installation on a virgin system, so I'm not sure if there is something else I might be missing. When I get a chance, I will try it again with a virgin installation.

You don't have Mountain Lion Server installed, do you? That's been challenging in the past, since the Server tools tries to take over and mess up everything one does from the terminal, particularly with Apache.

If you do figure out the problem, please let me know and I will update my installation guide.


On Apr 30, 2013, at 2:08 PM, "Fang, Jianwen" <[hidden email]> wrote:

> I can see in /etc/apache2/other/gbrowse2.conf:
>
> Alias        "/gbrowse2/i/" "/var/tmp/gbrowse2/images/"
> Alias        "/gbrowse2"    "/Library/Webserver/Documents/gbrowse2"
> ScriptAlias  "/gb2"      "/Library/Webserver/CGI-Executables/gb2"
>
> Also modified the following section to:
>
> <IfModule mod_fcgid.c>
>  Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
>  <Location /fgb2>
>    SetHandler   fcgid-script
>  </Location>
>  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>  # these directives prevent idle/busy timeouts and may need to be
>  # adjusted up or down
>  FcgidMinProcessesPerClass 6
>  FcgidIOTimeout   3600
>  FcgidBusyTimeout 3600
>  FcgidMaxRequestLen 2000000000
> </IfModule>
>
>
> I then restarted apache but still get permission error to:
> http://localhost/gb2/gbrowse/yeast
>
> But http://localhost/cgi-bin/gb2/gbrowse/yeast/ works just fine.  I guess
> it has something to do with alias /gb2 /cgi-bin/gb2.  The fastCGI may work
> once this problem is solved.
>
> Thanks again,
> JF
>
>
>
>
>
>
> On 4/30/13 1:55 PM, "Timothy Parnell" <[hidden email]> wrote:
>
>> Yes, it looks like you have FastCGI installed.
>> I agree, there's something wrong with the aliases.
>>
>> Both of these should work, and should indicate the aliases were loaded.
>> http://localhost/gb2/gbrowse/yeast
>> http://localhost/fgb2/gbrowse/yeast
>>
>> The gb2 alias is at the top of the file /etc/apache2/other/gbrowse2.conf.
>>
>> The fgb2 alias is in the <IfModule mod_fcgid.c> stanza. Here is mine.
>>
>> <IfModule mod_fcgid.c>
>> Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
>> <Location /fgb2>
>>   SetHandler   fcgid-script
>> </Location>
>> FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>> # these directives prevent idle/busy timeouts and may need to be
>> # adjusted up or down
>> FcgidMinProcessesPerClass 6
>> FcgidIOTimeout   3600
>> FcgidBusyTimeout 3600
>> FcgidMaxRequestLen 2000000000
>> </IfModule>
>>
>> If you don't see this, you can try running the following command again in
>> the GBrowse source directory
>> ./Build apache_conf
>> The output would become the contents of /etc/apache2/other/gbrowse2.conf
>>
>> Make sure the file is readable by all
>> sudo chmod -R +r /etc/apache2/other/
>>
>> Also, make sure at the bottom of /etc/apache2/httpd.conf, you are loading
>> all other confs. You should see
>> Include /private/etc/apache2/other/*.conf
>>
>> One other thing. I don't know if this should make a difference or not,
>> but the OS X sets the apache user to be
>> "_www"  and group "_www". The GBrowse installer assumes "www". This may
>> interfere with some things,
>> especially when the installer adjusts directory permissions. I have more
>> details in the "Install GBrowse"
>> section of my guide.
>>
>> ________________________________________
>> From: Fang, Jianwen [[hidden email]]
>> Sent: Tuesday, April 30, 2013 12:12 PM
>> To: Timothy Parnell
>> Cc: [hidden email]
>> Subject: Re: grows permission issue for OSX
>>
>> Dear Tim,
>>
>> Thanks very much for your quick response.  To answer your questions, yes,
>> I have modified the /etc/apache2/other/gbrowse2.conf to:
>>
>> <Directory "/Library/Webserver/CGI-Executables/gb2">
>>
>> Options ExecCGI
>> SetEnv GBROWSE_CONF   "/etc/gbrowse2"
>> #extra permissions
>> Order allow,deny
>> Allow from all
>> </Directory>
>>
>>
>>
>> Also I can see /usr/libexec/apache2/mod_fcgid.so, which is also included
>> in /etc/apache2/httpd.conf:
>>
>> LoadModule fcgid_module libexec/apache2/mod_fcgid.so
>>
>> I have restarted apache and can see in the error.log:
>>
>> [Tue Apr 30 12:57:34 2013] [notice] Apache/2.2.22 (Unix) DAV/2
>> mod_fcgid/2.3.7 mod_ssl/2.2.22 OpenSSL/0.9.8r configured -- resuming
>> normal operations
>>
>> I guess factCGI works.
>>
>> Run "sudo apachectl configtest" return "Syntax OK"
>>
>> Do you think it has anything to do with setting /gb2 as an alternative to
>> /cgi-bin/gb2?
>>
>> http://localhost/cgi-bin/gb2/gbrowse/yeast/ works in my system, but I get
>> permission issue for the followings:
>>
>> http://localhost/gb2/gbrowse/yeast
>> http://localhost/fgb2/gbrowse/yeast
>>
>> And http://localhost/cgi-bin/fgb2/gbrowse/yeast/ was not found.
>>
>> If so, could you please let me know how to set the alias?
>>
>> Thanks again,
>> JF
>>
>>
>>
>>
>>
>>
>>
>> On 4/30/13 12:17 PM, "Timothy Parnell" <[hidden email]>
>> wrote:
>>
>>> Hi,
>>>
>>> When you said you modified gbrowse2.conf, are you referring to
>>> /etc/apache2/other/gbrowse2.conf ?
>>> This requires that you add extra permissions to allow fastCGI to work as
>>> described in my wiki.
>>>
>>> A few other questions....
>>>
>>> Are you sure you installed FastCGI (OS X 10.8 doesn't include it by
>>> default)? You should have the file
>>> /usr/libexec/apache2/mod_fcgid.so
>>> and /etc/apache2/httpd.conf should be updated to include it.
>>>
>>> Did you make sure you restart apache? You should see a notice in your
>>> /var/log/apache2/error.log referencing mod_fcgid when you restart apache.
>>>
>>> Did you try running apachectl configtest to check the syntax?
>>>
>>> The instructions I've written mirror what I have on my system. Although
>>> it is possible that through upgrades from 10.6 -> 10.7 -> 10.8 there is
>>> something lurking in a dark directory in the depths of my system that I
>>> have overlooked.
>>>
>>> Tim
>>>
>>>
>>>
>>> ________________________________
>>> From: Fang, Jianwen [[hidden email]]
>>> Sent: Monday, April 29, 2013 8:46 PM
>>> To: Amelia Ireland
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] grows permission issue for OSX
>>>
>>> Thanks Amelia.  It works once I revised https.conf.
>>> Now I am trying to enable fastCGI.
>>> I follow the procedure described in
>>> http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_10
>>> .
>>> 8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get
>>> similar 403 error:  You don't have permission to access /fgb2/gbrowse/ on
>>> this server.  I guess I have missed some steps.  Could any one give me
>>> some advice?
>>>
>>> Thanks again,
>>> JF
>>>
>>>
>>>
>>> From: Amelia Ireland
>>> <[hidden email]<mailto:[hidden email]>>
>>> Date: Sunday, April 28, 2013 3:17 PM
>>> To: Jianwen Fang <[hidden email]<mailto:[hidden email]>>
>>> Cc:
>>> "[hidden email]<mailto:[hidden email]
>>> .
>>> net>"
>>> <[hidden email]<mailto:[hidden email]
>>> .
>>> net>>
>>> Subject: Re: grows permission issue for OSX
>>>
>>> Hello J Fang,
>>>
>>> Have you configured Apache (through the httpd.conf file) to allow access
>>> to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN will
>>> install the Perl modules, but you still need to set up Apache.
>>>
>>> I've cc'd the GBrowse mailing list; please keep it cc'd in your response
>>> as other list members may have advice.
>>>
>>> Thanks!
>>>
>>>
>>> On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen
>>> <[hidden email]<mailto:[hidden email]>> wrote:
>>> Hello there,
>>>
>>> I have been trying to install Gbrowse through CPAN in my Macbook Pro (OSX
>>> 10.8.3).  It keeps giving me the following error message when I access
>>> the example yeast dataset:
>>> Forbidden
>>> You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this
>>> server.
>>>
>>> It gives me the same error even after I chmod
>>> /var/lib/gbrowse2/databases/ and /Library/WebServer/CGI-Executables/gb2
>>> to 777.
>>>
>>> Could you let me know how I can fix the problem.
>>>
>>> Thanks very much in advance,
>>> J Fang
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Amelia Ireland
>>> GMOD Community Support
>>> http://gmod.org || @gmodproject
>>>
>>>
>>
>>
>>
>
>


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Re: grows permission issue for OSX

Fang, Jianwen
It is just a regular Retina Macbook pro.  I will definitely get back to
you if I find a solution.
Thanks a lot for your time and efforts!

On 4/30/13 4:00 PM, "Timothy Parnell" <[hidden email]> wrote:

>Hmmm. that's troubling, as I'm not sure what else to suggest. I haven't
>had a chance to try the full installation on a virgin system, so I'm not
>sure if there is something else I might be missing. When I get a chance,
>I will try it again with a virgin installation.
>
>You don't have Mountain Lion Server installed, do you? That's been
>challenging in the past, since the Server tools tries to take over and
>mess up everything one does from the terminal, particularly with Apache.
>
>If you do figure out the problem, please let me know and I will update my
>installation guide.
>
>
>On Apr 30, 2013, at 2:08 PM, "Fang, Jianwen" <[hidden email]> wrote:
>
>> I can see in /etc/apache2/other/gbrowse2.conf:
>>
>> Alias        "/gbrowse2/i/" "/var/tmp/gbrowse2/images/"
>> Alias        "/gbrowse2"    "/Library/Webserver/Documents/gbrowse2"
>> ScriptAlias  "/gb2"      "/Library/Webserver/CGI-Executables/gb2"
>>
>> Also modified the following section to:
>>
>> <IfModule mod_fcgid.c>
>>  Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
>>  <Location /fgb2>
>>    SetHandler   fcgid-script
>>  </Location>
>>  FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>>  # these directives prevent idle/busy timeouts and may need to be
>>  # adjusted up or down
>>  FcgidMinProcessesPerClass 6
>>  FcgidIOTimeout   3600
>>  FcgidBusyTimeout 3600
>>  FcgidMaxRequestLen 2000000000
>> </IfModule>
>>
>>
>> I then restarted apache but still get permission error to:
>> http://localhost/gb2/gbrowse/yeast
>>
>> But http://localhost/cgi-bin/gb2/gbrowse/yeast/ works just fine.  I
>>guess
>> it has something to do with alias /gb2 /cgi-bin/gb2.  The fastCGI may
>>work
>> once this problem is solved.
>>
>> Thanks again,
>> JF
>>
>>
>>
>>
>>
>>
>> On 4/30/13 1:55 PM, "Timothy Parnell" <[hidden email]>
>>wrote:
>>
>>> Yes, it looks like you have FastCGI installed.
>>> I agree, there's something wrong with the aliases.
>>>
>>> Both of these should work, and should indicate the aliases were loaded.
>>> http://localhost/gb2/gbrowse/yeast
>>> http://localhost/fgb2/gbrowse/yeast
>>>
>>> The gb2 alias is at the top of the file
>>>/etc/apache2/other/gbrowse2.conf.
>>>
>>> The fgb2 alias is in the <IfModule mod_fcgid.c> stanza. Here is mine.
>>>
>>> <IfModule mod_fcgid.c>
>>> Alias /fgb2 "/Library/Webserver/CGI-Executables/gb2"
>>> <Location /fgb2>
>>>   SetHandler   fcgid-script
>>> </Location>
>>> FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>>> # these directives prevent idle/busy timeouts and may need to be
>>> # adjusted up or down
>>> FcgidMinProcessesPerClass 6
>>> FcgidIOTimeout   3600
>>> FcgidBusyTimeout 3600
>>> FcgidMaxRequestLen 2000000000
>>> </IfModule>
>>>
>>> If you don't see this, you can try running the following command again
>>>in
>>> the GBrowse source directory
>>> ./Build apache_conf
>>> The output would become the contents of
>>>/etc/apache2/other/gbrowse2.conf
>>>
>>> Make sure the file is readable by all
>>> sudo chmod -R +r /etc/apache2/other/
>>>
>>> Also, make sure at the bottom of /etc/apache2/httpd.conf, you are
>>>loading
>>> all other confs. You should see
>>> Include /private/etc/apache2/other/*.conf
>>>
>>> One other thing. I don't know if this should make a difference or not,
>>> but the OS X sets the apache user to be
>>> "_www"  and group "_www". The GBrowse installer assumes "www". This may
>>> interfere with some things,
>>> especially when the installer adjusts directory permissions. I have
>>>more
>>> details in the "Install GBrowse"
>>> section of my guide.
>>>
>>> ________________________________________
>>> From: Fang, Jianwen [[hidden email]]
>>> Sent: Tuesday, April 30, 2013 12:12 PM
>>> To: Timothy Parnell
>>> Cc: [hidden email]
>>> Subject: Re: grows permission issue for OSX
>>>
>>> Dear Tim,
>>>
>>> Thanks very much for your quick response.  To answer your questions,
>>>yes,
>>> I have modified the /etc/apache2/other/gbrowse2.conf to:
>>>
>>> <Directory "/Library/Webserver/CGI-Executables/gb2">
>>>
>>> Options ExecCGI
>>> SetEnv GBROWSE_CONF   "/etc/gbrowse2"
>>> #extra permissions
>>> Order allow,deny
>>> Allow from all
>>> </Directory>
>>>
>>>
>>>
>>> Also I can see /usr/libexec/apache2/mod_fcgid.so, which is also
>>>included
>>> in /etc/apache2/httpd.conf:
>>>
>>> LoadModule fcgid_module libexec/apache2/mod_fcgid.so
>>>
>>> I have restarted apache and can see in the error.log:
>>>
>>> [Tue Apr 30 12:57:34 2013] [notice] Apache/2.2.22 (Unix) DAV/2
>>> mod_fcgid/2.3.7 mod_ssl/2.2.22 OpenSSL/0.9.8r configured -- resuming
>>> normal operations
>>>
>>> I guess factCGI works.
>>>
>>> Run "sudo apachectl configtest" return "Syntax OK"
>>>
>>> Do you think it has anything to do with setting /gb2 as an alternative
>>>to
>>> /cgi-bin/gb2?
>>>
>>> http://localhost/cgi-bin/gb2/gbrowse/yeast/ works in my system, but I
>>>get
>>> permission issue for the followings:
>>>
>>> http://localhost/gb2/gbrowse/yeast
>>> http://localhost/fgb2/gbrowse/yeast
>>>
>>> And http://localhost/cgi-bin/fgb2/gbrowse/yeast/ was not found.
>>>
>>> If so, could you please let me know how to set the alias?
>>>
>>> Thanks again,
>>> JF
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 4/30/13 12:17 PM, "Timothy Parnell" <[hidden email]>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> When you said you modified gbrowse2.conf, are you referring to
>>>> /etc/apache2/other/gbrowse2.conf ?
>>>> This requires that you add extra permissions to allow fastCGI to work
>>>>as
>>>> described in my wiki.
>>>>
>>>> A few other questions....
>>>>
>>>> Are you sure you installed FastCGI (OS X 10.8 doesn't include it by
>>>> default)? You should have the file
>>>> /usr/libexec/apache2/mod_fcgid.so
>>>> and /etc/apache2/httpd.conf should be updated to include it.
>>>>
>>>> Did you make sure you restart apache? You should see a notice in your
>>>> /var/log/apache2/error.log referencing mod_fcgid when you restart
>>>>apache.
>>>>
>>>> Did you try running apachectl configtest to check the syntax?
>>>>
>>>> The instructions I've written mirror what I have on my system.
>>>>Although
>>>> it is possible that through upgrades from 10.6 -> 10.7 -> 10.8 there
>>>>is
>>>> something lurking in a dark directory in the depths of my system that
>>>>I
>>>> have overlooked.
>>>>
>>>> Tim
>>>>
>>>>
>>>>
>>>> ________________________________
>>>> From: Fang, Jianwen [[hidden email]]
>>>> Sent: Monday, April 29, 2013 8:46 PM
>>>> To: Amelia Ireland
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] grows permission issue for OSX
>>>>
>>>> Thanks Amelia.  It works once I revised https.conf.
>>>> Now I am trying to enable fastCGI.
>>>> I follow the procedure described in
>>>>
>>>>http://code.google.com/p/biotoolbox/wiki/SetupForMacOSX#Notes_for_OS_X_
>>>>10
>>>> .
>>>> 8_Mountain_Lion and modified gbrowse2.conf accordingly.  But I get
>>>> similar 403 error:  You don't have permission to access
>>>>/fgb2/gbrowse/ on
>>>> this server.  I guess I have missed some steps.  Could any one give me
>>>> some advice?
>>>>
>>>> Thanks again,
>>>> JF
>>>>
>>>>
>>>>
>>>> From: Amelia Ireland
>>>> <[hidden email]<mailto:[hidden email]>>
>>>> Date: Sunday, April 28, 2013 3:17 PM
>>>> To: Jianwen Fang <[hidden email]<mailto:[hidden email]>>
>>>> Cc:
>>>>
>>>>"[hidden email]<mailto:[hidden email]
>>>>ge
>>>> .
>>>> net>"
>>>>
>>>><[hidden email]<mailto:[hidden email]
>>>>ge
>>>> .
>>>> net>>
>>>> Subject: Re: grows permission issue for OSX
>>>>
>>>> Hello J Fang,
>>>>
>>>> Have you configured Apache (through the httpd.conf file) to allow
>>>>access
>>>> to /cgi-bin/gb2/gbrowse and then restarted the Apache server? CPAN
>>>>will
>>>> install the Perl modules, but you still need to set up Apache.
>>>>
>>>> I've cc'd the GBrowse mailing list; please keep it cc'd in your
>>>>response
>>>> as other list members may have advice.
>>>>
>>>> Thanks!
>>>>
>>>>
>>>> On Sun, Apr 28, 2013 at 11:26 AM, Fang, Jianwen
>>>> <[hidden email]<mailto:[hidden email]>> wrote:
>>>> Hello there,
>>>>
>>>> I have been trying to install Gbrowse through CPAN in my Macbook Pro
>>>>(OSX
>>>> 10.8.3).  It keeps giving me the following error message when I access
>>>> the example yeast dataset:
>>>> Forbidden
>>>> You don't have permission to access /cgi-bin/gb2/gbrowse/yeast on this
>>>> server.
>>>>
>>>> It gives me the same error even after I chmod
>>>> /var/lib/gbrowse2/databases/ and
>>>>/Library/WebServer/CGI-Executables/gb2
>>>> to 777.
>>>>
>>>> Could you let me know how I can fix the problem.
>>>>
>>>> Thanks very much in advance,
>>>> J Fang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Amelia Ireland
>>>> GMOD Community Support
>>>> http://gmod.org || @gmodproject
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>



------------------------------------------------------------------------------
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Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap1
_______________________________________________
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