Tripti Grover | 4 Jan 2010 12:59

How to change the background color of details section

Hi...

I uploaded expression profile for my data ranging from 0-14 using the glyph wiggle_density in red color. However, for low expression values the lightest shade of red changes to white and disappears because the background of the details section is white in color, i want to have a contrasting background of the details section particularly for the transcription profile track, so that visibility is maintained even for low values.....how can i implement this??

In which file do i need to make modifications so that the background color for only transcriptional profile track can be changed??

Thanks in advance

--
Tripti

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Siddhartha Basu | 4 Jan 2010 15:47

turn off hsp grouping

Hi, 
How do i turn off grouping of HSP(show in separate tracks) in gbrowse 
from a tblastn result where the HSPs
belongs to the same hit but aligns to different strand of query(one if
+1 and other is -1). And i want this only for this kind of HSPs,  the
rest of them should work with the default settings. I am using chado
database with the gbrowse adaptor and for this display here is the
relevant config ....

[Blast_alignments]
feature       = "protein_match"
glyph         = transcript2
bgcolor       = blue
fgcolor       = black
height        = 7
stranded      = 1
maxdepth      = 2
key           = TBLASTN Alignments 

Is there any tweak in the config or callback i could use to do that.

thanks, 
-siddhartha

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Lincoln Stein | 4 Jan 2010 15:54

Re: How to change the background color of details section

Hi Tripti,

Currently you can only change the background color of the entire details section, which you do using the option "detail bgcolor".

I've also been annoyed at this behavior in the various density glyphs and plan to modify this family of glyphs so that the lightest color is still visible against a white background.

Lincoln

On Mon, Jan 4, 2010 at 6:59 AM, Tripti Grover <tripti.grover-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hi...

I uploaded expression profile for my data ranging from 0-14 using the glyph wiggle_density in red color. However, for low expression values the lightest shade of red changes to white and disappears because the background of the details section is white in color, i want to have a contrasting background of the details section particularly for the transcription profile track, so that visibility is maintained even for low values.....how can i implement this??

In which file do i need to make modifications so that the background color for only transcriptional profile track can be changed??

Thanks in advance

--
Tripti

--
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 <Renata.Musa-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>

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Lincoln Stein | 4 Jan 2010 16:02

Re: How to change the background color of details section

Just a thought. If you set the min_score value of the track to a level below the actual minimum value of the data, then the track will never go to complete white.

Lincoln

On Mon, Jan 4, 2010 at 6:59 AM, Tripti Grover <tripti.grover-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hi...

I uploaded expression profile for my data ranging from 0-14 using the glyph wiggle_density in red color. However, for low expression values the lightest shade of red changes to white and disappears because the background of the details section is white in color, i want to have a contrasting background of the details section particularly for the transcription profile track, so that visibility is maintained even for low values.....how can i implement this??

In which file do i need to make modifications so that the background color for only transcriptional profile track can be changed??

Thanks in advance

--
Tripti

------------------------------------------------------------------------------
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Farrer, Rhys | 4 Jan 2010 16:21

having troubles getting gbrowse to work

Dear Gbrowse,

I think I have installed everything I need to have gbrowse working (perl, GD, bioperl). I have started the tutorial webpage and on the 1st section making the volvox directory and copying the conf file to the right place. However, the volvox page shows up as:

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, you-hcDgGtZH8xNBDgjK7y7TUQ@public.gmane.org and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.

Below is a copy of the error_log that I found in ./private/var/log/apache2/error_log (if this means or explains much to you). Any help or hints would be greatly appreciated.

Thanks

Rhys Farrer

[Fri Dec 18 15:04:25 2009] [warn] Init: Session Cache is not configured [hint: SSLSessionCache]

[Fri Dec 18 15:04:26 2009] [notice] Digest: generating secret for digest authentication ...

[Fri Dec 18 15:04:26 2009] [notice] Digest: done

[Fri Dec 18 15:04:26 2009] [notice] Apache/2.2.13 (Unix) mod_ssl/2.2.13 OpenSSL/0.9.8k DAV/2 configured -- resuming normal operations

[Fri Dec 18 15:04:33 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/favicon.ico

[Fri Dec 18 15:04:36 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/favicon.ico

[Fri Dec 18 15:06:26 2009] [error] [client ::1] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 15:06:27 2009] [error] [client ::1] File does not exist: /Library/WebServer/Documents/favicon.ico

[Fri Dec 18 15:06:30 2009] [error] [client ::1] File does not exist: /Library/WebServer/Documents/favicon.ico

[Fri Dec 18 15:06:42 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 15:06:46 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 15:06:48 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 15:06:56 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 18:05:56 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 18:08:22 2009] [error] [client 10.0.3.43] File does not exist: /Library/WebServer/Documents/gbrowse

[Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Can't locate CGI/Session.pm in <at> INC ( <at> INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN failed--compilation aborted at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Compilation failed in require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Premature end of script headers: gbrowse, referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:18:29 2009] [error] [client 10.0.3.13] File does not exist: /Library/WebServer/Documents/favicon.ico

[Fri Dec 18 18:18:32 2009] [error] [client 10.0.3.13] File does not exist: /Library/WebServer/Documents/favicon.ico

[Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Can't locate CGI/Session.pm in <at> INC ( <at> INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN failed--compilation aborted at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Compilation failed in require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Premature end of script headers: gbrowse, referer: http://10.0.3.43/gbrowse/

[Fri Dec 18 18:46:54 2009] [error] [client ::1] Can't locate CGI/Session.pm in <at> INC ( <at> INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192.

[Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation aborted at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192.

[Fri Dec 18 18:46:54 2009] [error] [client ::1] Compilation failed in require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192.

[Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192.

[Fri Dec 18 18:46:54 2009] [error] [client ::1] Premature end of script headers: gbrowse

[Mon Jan 04 12:40:40 2010] [error] [client ::1] Can't locate CGI/Session.pm in <at> INC ( <at> INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192.

[Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation aborted at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192.

[Mon Jan 04 12:40:40 2010] [error] [client ::1] Compilation failed in require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192.

[Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192.

[Mon Jan 04 12:40:40 2010] [error] [client ::1] Premature end of script headers: gbrowse

[Mon Jan 04 12:40:40 2010] [error] [client ::1] File does not exist: /Library/WebServer/Documents/favicon.ico

[Mon Jan 04 12:40:43 2010] [error] [client ::1] File does not exist: /Library/WebServer/Documents/favicon.ico

[Mon Jan 04 13:04:16 2010] [error] [client ::1] Can't locate CGI/Session.pm in <at> INC ( <at> INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192.

[Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation aborted at /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm line 5, <DATA> line 192.

[Mon Jan 04 13:04:16 2010] [error] [client ::1] Compilation failed in require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192.

[Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line 192.

[Mon Jan 04 13:04:16 2010] [error] [client ::1] Premature end of script headers: gbrowse

[Mon Jan 04 13:05:10 2010] [error] [client 10.0.1.2] File does not exist: /Library/WebServer/Documents/favicon.ico

[Mon Jan 04 13:05:13 2010] [error] [client 10.0.1.2] File does not exist: /Library/WebServer/Documents/favicon.ico

[Mon Jan 04 13:21:12 2010] [error] [client ::1] Can't locate CGI/Session.pm in <at> INC ( <at> INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5

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Scott Cain | 4 Jan 2010 16:57

Re: having troubles getting gbrowse to work

Hello Rhys,

The error log indicates that you either didn't install CGI::Session,
or it didn't get installed properly.  How did you install GBrowse?
Did you use the net installer?

Scott

On Mon, Jan 4, 2010 at 10:21 AM, Farrer, Rhys <r.farrer09@...> wrote:
> Dear Gbrowse,
> I think I have installed everything I need to have gbrowse working (perl,
> GD, bioperl). I have started the tutorial webpage and on the 1st section
> making the volvox directory and copying the conf file to the right place.
> However, the volvox page shows up as:
>
> Internal Server Error
>
> The server encountered an internal error or misconfiguration and was unable
> to complete your request.
>
> Please contact the server administrator, you@... and inform
them of
> the time the error occurred, and anything you might have done that may have
> caused the error.
>
> More information about this error may be available in the server error log.
>
> Below is a copy of the error_log that I found in
> ./private/var/log/apache2/error_log (if this means or explains much to you).
> Any help or hints would be greatly appreciated.
> Thanks
> Rhys Farrer
>
> [Fri Dec 18 15:04:25 2009] [warn] Init: Session Cache is not configured
> [hint: SSLSessionCache]
> [Fri Dec 18 15:04:26 2009] [notice] Digest: generating secret for digest
> authentication ...
> [Fri Dec 18 15:04:26 2009] [notice] Digest: done
> [Fri Dec 18 15:04:26 2009] [notice] Apache/2.2.13 (Unix) mod_ssl/2.2.13
> OpenSSL/0.9.8k DAV/2 configured -- resuming normal operations
> [Fri Dec 18 15:04:33 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Fri Dec 18 15:04:36 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Fri Dec 18 15:06:26 2009] [error] [client ::1] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 15:06:27 2009] [error] [client ::1] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Fri Dec 18 15:06:30 2009] [error] [client ::1] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Fri Dec 18 15:06:42 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 15:06:46 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 15:06:48 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 15:06:56 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 18:05:56 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 18:08:22 2009] [error] [client 10.0.3.43] File does not exist:
> /Library/WebServer/Documents/gbrowse
> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Can't locate
> CGI/Session.pm in  <at> INC ( <at> INC contains:
> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN
> failed--compilation aborted at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Compilation failed in
> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN
> failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse
> line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Premature end of
> script headers: gbrowse, referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:18:29 2009] [error] [client 10.0.3.13] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Fri Dec 18 18:18:32 2009] [error] [client 10.0.3.13] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Can't locate
> CGI/Session.pm in  <at> INC ( <at> INC contains:
> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN
> failed--compilation aborted at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Compilation failed in
> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN
> failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse
> line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Premature end of
> script headers: gbrowse, referer: http://10.0.3.43/gbrowse/
> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Can't locate CGI/Session.pm
> in  <at> INC ( <at> INC contains:
> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192.
> [Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation
> aborted at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192.
> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Compilation failed in
> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192.
> [Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation
> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192.
> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Premature end of script
> headers: gbrowse
> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Can't locate CGI/Session.pm
> in  <at> INC ( <at> INC contains:
> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192.
> [Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation
> aborted at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192.
> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Compilation failed in
> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192.
> [Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation
> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192.
> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Premature end of script
> headers: gbrowse
> [Mon Jan 04 12:40:40 2010] [error] [client ::1] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Mon Jan 04 12:40:43 2010] [error] [client ::1] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Can't locate CGI/Session.pm
> in  <at> INC ( <at> INC contains:
> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
> /Network/Library/Perl/5.10.0 /Network/Library/Perl
> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.10.0 .) at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192.
> [Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation
> aborted at
> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
> line 5, <DATA> line 192.
> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Compilation failed in
> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192.
> [Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation
> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
> 192.
> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Premature end of script
> headers: gbrowse
> [Mon Jan 04 13:05:10 2010] [error] [client 10.0.1.2] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Mon Jan 04 13:05:13 2010] [error] [client 10.0.1.2] File does not exist:
> /Library/WebServer/Documents/favicon.ico
> [Mon Jan 04 13:21:12 2010] [error] [client ::1] Can't locate CGI/Session.pm
> in  <at> INC ( <at> INC contains:
> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
> /Library/Perl/Updates/5.10.0
> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
> /Library/Perl/5.10.0 /Network/Library/Perl/5
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
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headers

Farrer, Rhys | 4 Jan 2010 17:43

Re: having troubles getting gbrowse to work

Brilliant! - Followed those instructions - and the Volvox page now comes up as it should do.
Thankyou!
Rhys

On 4 Jan 2010, at 16:37, Scott Cain wrote:

> Hi Rhys,
>
> Please keep your responses on the GBrowse mailing list.
>
> You do need ./Build install, but it apparently failed to install.
> What is not clear to me is why it is failing to install ("Already
> tried without success").  Perhaps you could get the tarball directly
> from CPAN and try installing it by hand:
>
> http://search.cpan.org/CPAN/authors/id/M/MA/MARKSTOS/CGI-Session-4.42.tar.gz
>
>  tar zxvf CGI-Session-4.42.tar.gz
>  cd CGI-Session-4.42
>  perl Build.PL
>  ./Build
>  ./Build test
>  sudo ./Build install --uninst 1
>
> Scott
>
> On Mon, Jan 4, 2010 at 11:12 AM, Farrer, Rhys <r.farrer09@...> wrote:
>> Hi Scott,
>>
>> I'm pretty sure I used the net installer! There was vast reams of information scrolling past on the
command terminal (in mac) when I was trying to install it.
>> I just tried to (re)install CGI::Session with "sudo CPAN CGI::Session".
>> It said:
>> Running Build test
>> Has already been tested successfully
>> Running Build install
>> Already tried without success
>>
>> so perhaps i need to "Build install"? To be honest I'm pretty lost with all of this!!
>> Cheers.
>> Rhys
>>
>> On 4 Jan 2010, at 15:57, Scott Cain wrote:
>>
>>> Hello Rhys,
>>>
>>> The error log indicates that you either didn't install CGI::Session,
>>> or it didn't get installed properly.  How did you install GBrowse?
>>> Did you use the net installer?
>>>
>>> Scott
>>>
>>> On Mon, Jan 4, 2010 at 10:21 AM, Farrer, Rhys
<r.farrer09@...> wrote:
>>>> Dear Gbrowse,
>>>> I think I have installed everything I need to have gbrowse working (perl,
>>>> GD, bioperl). I have started the tutorial webpage and on the 1st section
>>>> making the volvox directory and copying the conf file to the right place.
>>>> However, the volvox page shows up as:
>>>>
>>>> Internal Server Error
>>>>
>>>> The server encountered an internal error or misconfiguration and was unable
>>>> to complete your request.
>>>>
>>>> Please contact the server administrator, you@... and
inform them of
>>>> the time the error occurred, and anything you might have done that may have
>>>> caused the error.
>>>>
>>>> More information about this error may be available in the server error log.
>>>>
>>>> Below is a copy of the error_log that I found in
>>>> ./private/var/log/apache2/error_log (if this means or explains much to you).
>>>> Any help or hints would be greatly appreciated.
>>>> Thanks
>>>> Rhys Farrer
>>>>
>>>> [Fri Dec 18 15:04:25 2009] [warn] Init: Session Cache is not configured
>>>> [hint: SSLSessionCache]
>>>> [Fri Dec 18 15:04:26 2009] [notice] Digest: generating secret for digest
>>>> authentication ...
>>>> [Fri Dec 18 15:04:26 2009] [notice] Digest: done
>>>> [Fri Dec 18 15:04:26 2009] [notice] Apache/2.2.13 (Unix) mod_ssl/2.2.13
>>>> OpenSSL/0.9.8k DAV/2 configured -- resuming normal operations
>>>> [Fri Dec 18 15:04:33 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Fri Dec 18 15:04:36 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Fri Dec 18 15:06:26 2009] [error] [client ::1] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 15:06:27 2009] [error] [client ::1] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Fri Dec 18 15:06:30 2009] [error] [client ::1] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Fri Dec 18 15:06:42 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 15:06:46 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 15:06:48 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 15:06:56 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 18:05:56 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 18:08:22 2009] [error] [client 10.0.3.43] File does not exist:
>>>> /Library/WebServer/Documents/gbrowse
>>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Can't locate
>>>> CGI/Session.pm in  <at> INC ( <at> INC contains:
>>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/Updates/5.10.0
>>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/Extras/5.10.0 .) at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN
>>>> failed--compilation aborted at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Compilation failed in
>>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN
>>>> failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse
>>>> line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Premature end of
>>>> script headers: gbrowse, referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:18:29 2009] [error] [client 10.0.3.13] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Fri Dec 18 18:18:32 2009] [error] [client 10.0.3.13] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Can't locate
>>>> CGI/Session.pm in  <at> INC ( <at> INC contains:
>>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/Updates/5.10.0
>>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/Extras/5.10.0 .) at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN
>>>> failed--compilation aborted at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Compilation failed in
>>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN
>>>> failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse
>>>> line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Premature end of
>>>> script headers: gbrowse, referer: http://10.0.3.43/gbrowse/
>>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Can't locate CGI/Session.pm
>>>> in  <at> INC ( <at> INC contains:
>>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/Updates/5.10.0
>>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/Extras/5.10.0 .) at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192.
>>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation
>>>> aborted at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192.
>>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Compilation failed in
>>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192.
>>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation
>>>> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192.
>>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Premature end of script
>>>> headers: gbrowse
>>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Can't locate CGI/Session.pm
>>>> in  <at> INC ( <at> INC contains:
>>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/Updates/5.10.0
>>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/Extras/5.10.0 .) at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192.
>>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation
>>>> aborted at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192.
>>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Compilation failed in
>>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192.
>>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation
>>>> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192.
>>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Premature end of script
>>>> headers: gbrowse
>>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Mon Jan 04 12:40:43 2010] [error] [client ::1] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Can't locate CGI/Session.pm
>>>> in  <at> INC ( <at> INC contains:
>>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/Updates/5.10.0
>>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/Extras/5.10.0 .) at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192.
>>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation
>>>> aborted at
>>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>>> line 5, <DATA> line 192.
>>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Compilation failed in
>>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192.
>>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation
>>>> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>>> 192.
>>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Premature end of script
>>>> headers: gbrowse
>>>> [Mon Jan 04 13:05:10 2010] [error] [client 10.0.1.2] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Mon Jan 04 13:05:13 2010] [error] [client 10.0.1.2] File does not exist:
>>>> /Library/WebServer/Documents/favicon.ico
>>>> [Mon Jan 04 13:21:12 2010] [error] [client ::1] Can't locate CGI/Session.pm
>>>> in  <at> INC ( <at> INC contains:
>>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/Updates/5.10.0
>>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>>> /Library/Perl/5.10.0 /Network/Library/Perl/5
>>>> ------------------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Verizon Developer Community
>>>> Take advantage of Verizon's best-in-class app development support
>>>> A streamlined, 14 day to market process makes app distribution fast and easy
>>>> Join now and get one step closer to millions of Verizon customers
>>>> http://p.sf.net/sfu/verizon-dev2dev
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> Gmod-gbrowse@...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev

headers

Scott Cain | 4 Jan 2010 17:37

Re: having troubles getting gbrowse to work

Hi Rhys,

Please keep your responses on the GBrowse mailing list.

You do need ./Build install, but it apparently failed to install.
What is not clear to me is why it is failing to install ("Already
tried without success").  Perhaps you could get the tarball directly
from CPAN and try installing it by hand:

http://search.cpan.org/CPAN/authors/id/M/MA/MARKSTOS/CGI-Session-4.42.tar.gz

  tar zxvf CGI-Session-4.42.tar.gz
  cd CGI-Session-4.42
  perl Build.PL
  ./Build
  ./Build test
  sudo ./Build install --uninst 1

Scott

On Mon, Jan 4, 2010 at 11:12 AM, Farrer, Rhys <r.farrer09@...> wrote:
> Hi Scott,
>
> I'm pretty sure I used the net installer! There was vast reams of information scrolling past on the command
terminal (in mac) when I was trying to install it.
> I just tried to (re)install CGI::Session with "sudo CPAN CGI::Session".
> It said:
> Running Build test
>  Has already been tested successfully
> Running Build install
>  Already tried without success
>
> so perhaps i need to "Build install"? To be honest I'm pretty lost with all of this!!
> Cheers.
> Rhys
>
> On 4 Jan 2010, at 15:57, Scott Cain wrote:
>
>> Hello Rhys,
>>
>> The error log indicates that you either didn't install CGI::Session,
>> or it didn't get installed properly.  How did you install GBrowse?
>> Did you use the net installer?
>>
>> Scott
>>
>> On Mon, Jan 4, 2010 at 10:21 AM, Farrer, Rhys <r.farrer09@...> wrote:
>>> Dear Gbrowse,
>>> I think I have installed everything I need to have gbrowse working (perl,
>>> GD, bioperl). I have started the tutorial webpage and on the 1st section
>>> making the volvox directory and copying the conf file to the right place.
>>> However, the volvox page shows up as:
>>>
>>> Internal Server Error
>>>
>>> The server encountered an internal error or misconfiguration and was unable
>>> to complete your request.
>>>
>>> Please contact the server administrator, you@... and
inform them of
>>> the time the error occurred, and anything you might have done that may have
>>> caused the error.
>>>
>>> More information about this error may be available in the server error log.
>>>
>>> Below is a copy of the error_log that I found in
>>> ./private/var/log/apache2/error_log (if this means or explains much to you).
>>> Any help or hints would be greatly appreciated.
>>> Thanks
>>> Rhys Farrer
>>>
>>> [Fri Dec 18 15:04:25 2009] [warn] Init: Session Cache is not configured
>>> [hint: SSLSessionCache]
>>> [Fri Dec 18 15:04:26 2009] [notice] Digest: generating secret for digest
>>> authentication ...
>>> [Fri Dec 18 15:04:26 2009] [notice] Digest: done
>>> [Fri Dec 18 15:04:26 2009] [notice] Apache/2.2.13 (Unix) mod_ssl/2.2.13
>>> OpenSSL/0.9.8k DAV/2 configured -- resuming normal operations
>>> [Fri Dec 18 15:04:33 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Fri Dec 18 15:04:36 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Fri Dec 18 15:06:26 2009] [error] [client ::1] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 15:06:27 2009] [error] [client ::1] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Fri Dec 18 15:06:30 2009] [error] [client ::1] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Fri Dec 18 15:06:42 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 15:06:46 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 15:06:48 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 15:06:56 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 18:05:56 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 18:08:22 2009] [error] [client 10.0.3.43] File does not exist:
>>> /Library/WebServer/Documents/gbrowse
>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Can't locate
>>> CGI/Session.pm in  <at> INC ( <at> INC contains:
>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/Updates/5.10.0
>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/Extras/5.10.0 .) at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN
>>> failed--compilation aborted at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Compilation failed in
>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] BEGIN
>>> failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse
>>> line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:09:19 2009] [error] [client 10.0.3.43] Premature end of
>>> script headers: gbrowse, referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:18:29 2009] [error] [client 10.0.3.13] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Fri Dec 18 18:18:32 2009] [error] [client 10.0.3.13] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Can't locate
>>> CGI/Session.pm in  <at> INC ( <at> INC contains:
>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/Updates/5.10.0
>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/Extras/5.10.0 .) at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN
>>> failed--compilation aborted at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Compilation failed in
>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] BEGIN
>>> failed--compilation aborted at /Library/WebServer/CGI-Executables/gbrowse
>>> line 23, <DATA> line 192., referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:39:38 2009] [error] [client 10.0.3.43] Premature end of
>>> script headers: gbrowse, referer: http://10.0.3.43/gbrowse/
>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Can't locate CGI/Session.pm
>>> in  <at> INC ( <at> INC contains:
>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/Updates/5.10.0
>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/Extras/5.10.0 .) at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192.
>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation
>>> aborted at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192.
>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Compilation failed in
>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192.
>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] BEGIN failed--compilation
>>> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192.
>>> [Fri Dec 18 18:46:54 2009] [error] [client ::1] Premature end of script
>>> headers: gbrowse
>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Can't locate CGI/Session.pm
>>> in  <at> INC ( <at> INC contains:
>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/Updates/5.10.0
>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/Extras/5.10.0 .) at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192.
>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation
>>> aborted at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192.
>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Compilation failed in
>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192.
>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] BEGIN failed--compilation
>>> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192.
>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] Premature end of script
>>> headers: gbrowse
>>> [Mon Jan 04 12:40:40 2010] [error] [client ::1] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Mon Jan 04 12:40:43 2010] [error] [client ::1] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Can't locate CGI/Session.pm
>>> in  <at> INC ( <at> INC contains:
>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/Updates/5.10.0
>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Network/Library/Perl/5.10.0 /Network/Library/Perl
>>> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/Extras/5.10.0 .) at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192.
>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation
>>> aborted at
>>> /Library/Perl/5.10.0/darwin-thread-multi-2level/Bio/Graphics/Browser/PageSettings.pm
>>> line 5, <DATA> line 192.
>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Compilation failed in
>>> require at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192.
>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] BEGIN failed--compilation
>>> aborted at /Library/WebServer/CGI-Executables/gbrowse line 23, <DATA> line
>>> 192.
>>> [Mon Jan 04 13:04:16 2010] [error] [client ::1] Premature end of script
>>> headers: gbrowse
>>> [Mon Jan 04 13:05:10 2010] [error] [client 10.0.1.2] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Mon Jan 04 13:05:13 2010] [error] [client 10.0.1.2] File does not exist:
>>> /Library/WebServer/Documents/favicon.ico
>>> [Mon Jan 04 13:21:12 2010] [error] [client ::1] Can't locate CGI/Session.pm
>>> in  <at> INC ( <at> INC contains:
>>> /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/Updates/5.10.0
>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level
>>> /Library/Perl/5.10.0 /Network/Library/Perl/5
>>> ------------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Verizon Developer Community
>>> Take advantage of Verizon's best-in-class app development support
>>> A streamlined, 14 day to market process makes app distribution fast and easy
>>> Join now and get one step closer to millions of Verizon customers
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>>> _______________________________________________
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>>> Gmod-gbrowse@...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
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headers

Richard Donald Hayes | 4 Jan 2010 18:52

Re: Is it possible to use an include type statement in conf files

Hi Scott,

Just to verify, is the include directive a Gbrowse 2 feature only? I have not had luck with trials on Gbrowse
1.69, and this is only mentioned in the Gbrowse2 config documentation.

Thanks,
Richard Hayes
Joint Genome Institute / Lawrence Berkeley National Lab

----- Original Message -----
From: Scott Cain <scott@...>
Date: Thursday, December 24, 2009 6:33 am
Subject: Re: [Gmod-gbrowse] Is it possible to use an include type statement	in conf files
To: Keiran Raine <kr2@...>
Cc: "Gbrowse (E-mail)" <gmod-gbrowse@...>

> Hi Keiran,
> 
> Include directives are supported.  All you need to do is this:
> 
> #include path/to/file
> 
> at the location where the included text should go.
> 
> Scott
> 
> 
> On Thu, Dec 24, 2009 at 4:21 AM, Keiran Raine <kr2@...> 
> wrote:> Hi,
> >
> > I have a standard set up for most of my tracks in gBrowse and a big
> > chunk of init_code for mouse over balloons.  This is the same for 
> each> datasource.
> >
> > Is it possible to import data as an include so this can be 
> updated in
> > a single file rather than in each conf file?
> >
> > Regards,
> >
> > Keiran Raine
> > Senior Computer Biologist
> > The Cancer Genome Project
> > Ext: 2100
> > kr2@...
> >
> > The Wellcome Trust Sanger Institute is operated by Genome Research
> > Limited, a charity registered in England with number 1021457 and a
> > company registered in England with number 2742969, whose registered
> > office is 215 Euston Road, London, NW1 2BE.
> >
> >
> >
> >
> >
> > --
> >  The Wellcome Trust Sanger Institute is operated by Genome Research
> >  Limited, a charity registered in England with number 1021457 and a
> >  company registered in England with number 2742969, whose registered
> >  office is 215 Euston Road, London, NW1 2BE.
> >
> > ------------------------------------------------------------------
> ------------
> > This SF.Net email is sponsored by the Verizon Developer Community
> > Take advantage of Verizon's best-in-class app development support
> > A streamlined, 14 day to market process makes app distribution 
> fast and easy
> > Join now and get one step closer to millions of Verizon customers
> > http://p.sf.net/sfu/verizon-dev2dev
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse@...
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> 
> 
> 
> -- 
> --------------------------------------------------------------------
> ----
> Scott Cain, Ph. D.                                   scott at 
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> --------------------------------------------------------------------
> ----------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast 
> and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev 
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> 

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
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headers

Scott Cain | 4 Jan 2010 19:08

Re: Is it possible to use an include type statement in conf files

Hi Richard,

I was just getting ready to write that it should still work with
GBrowse 1.69/1.70 and Bioperl 1.6 or better, but I can't get it to
work right now with 1.70 and BP 1.6.1, so I'm looking into it now.

Scott

On Mon, Jan 4, 2010 at 12:52 PM, Richard Donald Hayes <RDHayes@...> wrote:
> Hi Scott,
>
> Just to verify, is the include directive a Gbrowse 2 feature only? I have not had luck with trials on Gbrowse
1.69, and this is only mentioned in the Gbrowse2 config documentation.
>
> Thanks,
> Richard Hayes
> Joint Genome Institute / Lawrence Berkeley National Lab
>
> ----- Original Message -----
> From: Scott Cain <scott@...>
> Date: Thursday, December 24, 2009 6:33 am
> Subject: Re: [Gmod-gbrowse] Is it possible to use an include type statement     in conf files
> To: Keiran Raine <kr2@...>
> Cc: "Gbrowse (E-mail)" <gmod-gbrowse@...>
>
>> Hi Keiran,
>>
>> Include directives are supported.  All you need to do is this:
>>
>> #include path/to/file
>>
>> at the location where the included text should go.
>>
>> Scott
>>
>>
>> On Thu, Dec 24, 2009 at 4:21 AM, Keiran Raine <kr2@...>
>> wrote:> Hi,
>> >
>> > I have a standard set up for most of my tracks in gBrowse and a big
>> > chunk of init_code for mouse over balloons.  This is the same for
>> each> datasource.
>> >
>> > Is it possible to import data as an include so this can be
>> updated in
>> > a single file rather than in each conf file?
>> >
>> > Regards,
>> >
>> > Keiran Raine
>> > Senior Computer Biologist
>> > The Cancer Genome Project
>> > Ext: 2100
>> > kr2@...
>> >
>> > The Wellcome Trust Sanger Institute is operated by Genome Research
>> > Limited, a charity registered in England with number 1021457 and a
>> > company registered in England with number 2742969, whose registered
>> > office is 215 Euston Road, London, NW1 2BE.
>> >
>> >
>> >
>> >
>> >
>> > --
>> >  The Wellcome Trust Sanger Institute is operated by Genome Research
>> >  Limited, a charity registered in England with number 1021457 and a
>> >  company registered in England with number 2742969, whose registered
>> >  office is 215 Euston Road, London, NW1 2BE.
>> >
>> > ------------------------------------------------------------------
>> ------------
>> > This SF.Net email is sponsored by the Verizon Developer Community
>> > Take advantage of Verizon's best-in-class app development support
>> > A streamlined, 14 day to market process makes app distribution
>> fast and easy
>> > Join now and get one step closer to millions of Verizon customers
>> > http://p.sf.net/sfu/verizon-dev2dev
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > Gmod-gbrowse@...
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>>
>>
>>
>> --
>> --------------------------------------------------------------------
>> ----
>> Scott Cain, Ph. D.                                   scott at
>> scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> --------------------------------------------------------------------
>> ----------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast
>> and easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>

--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
This SF.Net email is sponsored by the Verizon Developer Community
Take advantage of Verizon's best-in-class app development support
A streamlined, 14 day to market process makes app distribution fast and easy
Join now and get one step closer to millions of Verizon customers
http://p.sf.net/sfu/verizon-dev2dev

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