[Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello


I've managed to install Jbrowse on my linux box, but somehow the tricks that
worked there don't seem to apply to the Mac. What are the minimal set of
Gbrowse libraries required for Jbrowse?

Installing GD with Fink was the only step that worked (see big rant below).

Is there a pre-packaged Gbrowse perl library that I can just download and
put in my PERL5LIB path to get Jbrowse running?

That would really make my day!

Thanks,

Isabelle


<big rant>
I've spent several hours trying to install Gbrowse on my mac (10.5.6) and
can't get it to go past the blasted cpan nightmare. Sorry, had to let my
frustration out. I really hate cpan with a vengance, and it probably knows
it ;-)

Errors are inconsistent: cpan can't install either LWP, or Harness, or GD,
or Compress::Zlib. I've first tried to execute the Gbrowse installer without
any options. It crashes with:

Force getting a BioPerl nightly build; the most recent release is too old

*** Installing BioPerl ***
Downloading bioperl-live...
Can't locate LWP.pm in @INC (@INC contains:
/System/Library/Perl/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
/Library/Perl/5.8.8 /Library/Perl
/Network/Library/Perl/5.8.8/darwin-thread-multi-2level
/Network/Library/Perl/5.8.8 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1)
at /System/Library/Perl/Extras/5.8.8/LWP/Simple.pm line 37.

I tried to install LWP from cpan and get:
Can't make directory /Users/iphan/.cpan/build/YAML-0.68 read+writeable:
Operation not permitted at /System/Library/Perl/5.8.8/CPAN.pm line 966

I understand that error means I shouldn't have run the gbrowse installer
script with 'sudo', but since it won't run otherwise, what the hell am I
supposed to do??! Manually do a chmod of .cpan after each installer crash?

 I've tried pre-installing Bioperl 7 times, from the tarball, from cpan,
from cvs, version 1.6.0, 1.5.x version, dev version (guess that's the same
as downloading from cvs?), bioperl-live. None of them seem to play with the
Gbrowse perl installer:

*** (back in Bioperl Build.PL) ***
Cannot chdir() back to /Users/iphan/.cpan/build/BioPerl-1.6.0: No such file
or directory at Bio/Root/Build.pm line 461.
Couldn't run Build.PL:
/System/Library/Perl/Extras/5.8.8/Module/Build/Compat.pm line 200.
Running make test
  Make had some problems, maybe interrupted? Won't test
Running make install
  Make had some problems, maybe interrupted? Won't install

</big rant>