Re: [Gmod-gbrowse] Problems installing gbrowse

[Todd H. <ha...@cs...>]

Peter -

First, have you tried building BioPerl from source using  
Module::Build instead of the Makefile.PL?

ie

perl ./Build
/Build test
[sudo] ./Build install

Second, what are the permissions on /etc/httpd/gbrowse.conf?  This  
directory needs to be readable by httpd, or more likely, nobody.

I routinely run GBrowse on OS X but I run my own custom apache and  
have a more linux-y style directory structure so these tips might not  
be completely accurate.

Todd

On Dec 18, 2006, at 1:47 PM, Peter Schattner wrote:

> Hello Lincoln et al
>
> I am trying to install & run gbrowse. I have been following the
> instructions in the gbrowse tutorial, but have encountered a problem
> (maybe more than one.) I am running Mac OS X 10.3 on a G5 desktop.
>
> Problem 1:
> When I run perl Makefile.PL:
> Generic-Genome-Browser-1.65$ perl Makefile.PL
> HTDOCS=/Library/WebServer/Documents CONF=/Library/WebServer/conf
> CGIBIN=/Library/WebServer/CGI-Executables
>
> I get:
>
> Warning: prerequisite Bio::Perl 1.5 not found. We have 1.0050021.
> dyld: perl Undefined symbols:
> _jpeg_resync_to_restart
> Trace/BPT trap
>
> Now I have installed the (unstable) bioperl-1.5.2 as required. When I
> examine the Bio::Perl module I see:
> # $Id: Perl.pm,v 1.26.4.4 2006/10/02 23:10:12 sendu Exp $
>
> so I don't understand the first warning. And frankly I don't  
> understand
> the remaining warnings either.
>
> Note that I did not use the 'LIB=/sw/lib/perl5' option in the perl
> Makefile.PL command mentioned in the README.Macosx file, since I  
> did not
> install the gdlib with fink and it is at /usr/local/lib. Also I  
> noticed
> that despite the CONF=/Library/WebServer/conf parameters the config
> directory actually wound up as /etc/httpd/gbrowse.conf/ so that's  
> where
> I put the volvox.conf file. Perhaps I screwed something up here?
>
> Problem 2.
> Anyway, since they were warnings and not errors, I thought I'd try to
> keep going. And actually the next parts of the installation seemed  
> to go
> OK until I actually tried to view the volvax browser where I got an
> "internal server error."
>
> Following the tutorial instructions I noted that volvox.conf and
> volvox1.gff files do exist and are in the directories I defined as
> $HTDOCS and $CONF
> ie:
> export HTDOCS='/Library/WebServer/Documents'
> export CONF='/etc/httpd/gbrowse.conf'
>
> The Apache error log had the following errors:
> /Library/WebServer/conf/gbrowse.conf: not a directory at
> /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/Graphics/Browser/ 
> Util.pm
> line 149
> [Mon Dec 18 11:23:11 2006] [error] [client 127.0.0.1] Premature end of
> script headers: /Library/WebServer/CGI-Executables/gbrowse
> [Mon Dec 18 11:23:11 2006] [error] [client 127.0.0.1] File does not
> exist: /Library/WebServer/Documents/favicon.ico
> [Mon Dec 18 11:23:59 2006] [error] [client 192.168.10.3] File does not
> exist: /Library/WebServer/Documents/favicon.ico
>
> Examining the Util.pm file indicates that line 149 is:
> $CONFIG->read_configuration($dir,$suffix) or die "Can't read
> configuration files: $!";
>
> which is presumably the problem, but I can't see what needs to be done
> to remedy the situation.
>
> Thanks in advance for any assistance you can provide.
>
> Peter
>
>
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