gmod-ajax

[Gmod-ajax] kudos!

[Jay H. <ja...@ja...>]

Can I just take a second to say "wow"!?

GBrowse is awesome. AJAX GBrowse is awesome + 1. Very impressive. I'll 
be trying to install it today.

Thanks for all your hard work!

j
seqlab.net
http://www.bioperl.org/wiki/User:Jhannah

Re: [Gmod-ajax] kudos!

[Mitch S. <mit...@be...>]

On Sat, 2007-04-07 at 13:15 -0500, Jay Hannah wrote:
> Can I just take a second to say "wow"!?
> 
> GBrowse is awesome. AJAX GBrowse is awesome + 1. Very impressive. I'll 
> be trying to install it today.

Cool!

The current documentation on the wiki about installing is out of date.
I'll be spending some time today updating the docs, but the gist of it
is that you need a recent bioperl, which you can install using CPAN like
so:
cpan[1]> install S/SE/SENDU/bioperl-1.5.2_102.tar.gz

And you also need a recent GBrowse; the version here should work:
http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513&release_id=491673
(if the URL wraps, you can also just go to gmod.org and follow the
GBrowse download link).

Actually installing GBrowse can be a little involved, but if you're just
interested in rendering tiles I believe you can just put the full path
to Generic-Genome-Browser-1.67/lib into your PERL5LIB environment
variable.  GBrowse also has some requirements that you should be able to
satisfy from CPAN.  The GBrowse requirements are listed at the gmod
site:
http://blog.gmod.org/gbrowse_installation
and from that page this is the list of required modules:
            CGI                  (2.56 or higher)
            GD                   (2.07 or higher)
            CGI::Session         (4.03 or higher)
            DBI                  (any version)
            DBD::mysql           (any version)
            Digest::MD5          (any version)
            Text::Shellwords     (any version)
            Class::Base          (any version)

And from their list of optional modules I believe we need the XML ones
and GD::SVG.

Sorry about the documentation being out of date; please do follow up to
the list with any problems you have.  When you're knee deep in it it's
easy to forget about the difficulties of getting started.

Regards,
Mitch

Re: [Gmod-ajax] kudos!

[Jay H. <ja...@ja...>]

On Apr 7, 2007, at 6:18 PM, Mitch Skinner wrote:
> Reading your email again, I see you've got plenty of experience with
> BioPerl.  Sorry if my last email was patronizing; I was thinking about
> how I'd update our installation documentation.

-laugh-  Not at all!  I've spent 6 hours this weekend fighting  
dependencies in the GD, lib*, Apache stacks. Always humbling. :)

Since I've got you, I'm guessing you have commit perms to the whole  
gbrowse project, so you might want to add "my " on line 29 to get rid  
of this error. I pulled trunk from CVS so I'm pretty sure this is  
just a simple vanilla bug:

[Sun Apr 08 08:58:10 2007] [error] [client 72.196.27.155] Global  
symbol "$obj" requires explicit package name at /usr/lib/perl5/ 
site_perl/5.8.6/x86_64-linux-thread-multi/Bio/Graphics/Browser/ 
PluginSet.pm line 29, <DATA> line 192.

Either the lib/ or libnew/ version(s)...?

Got gbrowse going, now on to AJAX!

Yee-ha!

j
seqlab.net
http://www.bioperl.org/wiki/User:Jhannah

Re: [Gmod-ajax] kudos!

[Mitch S. <mit...@be...>]

On Sun, 2007-04-08 at 09:42 -0500, Jay Hannah wrote:
> Since I've got you, I'm guessing you have commit perms to the whole  
> gbrowse project, so you might want to add "my " on line 29 to get rid  
> of this error. I pulled trunk from CVS so I'm pretty sure this is  
> just a simple vanilla bug:

I mostly just stay in my little ajax sandbox; if I wanted to get a patch
in anywhere else I'd bring it up on the mailing lists first, so I'd
prefer if you raised this on gmod-gbrowse along with your other stuff.

> Either the lib/ or libnew/ version(s)...?

FWIW, it seems like the stable branch is the better one to work with at
the moment.

Mitch