[GMOD-devel] Help with Gbrowse2.0 on Solaris

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[GMOD-devel] Help with Gbrowse2.0 on Solaris

Jayaraman, Pushkala

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast

 

But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:

 

 

[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network

 

 

We are currently installing this on a Solaris system. Please help me figure out this error..

 

 

Thanks,

Pushkala


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Re: [GMOD-devel] [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

Lincoln Stein
The problem is an out-of-date Bio::Graphics. The install should have complained that you need a more recent version. Please install Bio::Graphics version 2.09.

Lincoln

On Mon, May 17, 2010 at 4:31 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast

 

But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:

 

 

[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network

 

 

We are currently installing this on a Solaris system. Please help me figure out this error..

 

 

Thanks,

Pushkala


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: [GMOD-devel] [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

Jayaraman, Pushkala

Thanks Lincoln,

Will do just that.

 

 

Pushkala

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, May 17, 2010 3:41 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

 

The problem is an out-of-date Bio::Graphics. The install should have complained that you need a more recent version. Please install Bio::Graphics version 2.09.

 

Lincoln

On Mon, May 17, 2010 at 4:31 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast

 

But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:

 

 

[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network

 

 

We are currently installing this on a Solaris system. Please help me figure out this error..

 

 

Thanks,

Pushkala


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


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