[Bioperl-l] Fwd: [Gmod-ajax] Jbrowse on mac os 10.5

Hilmar Lapp hlapp at gmx.net
Sun Mar 15 09:27:28 EDT 2009

Just forwarding this here in case someone has a moment to check  
whether there might be anything here that can be improved from the  
BioPerl side of things. (Note that in Isabelle's case she wouldn't  
need to install GBrowse and BioPerl in concert.)


Begin forwarded message:

From: iphan <isabelle.phan at sbri.org>
Date: March 15, 2009 12:29:10 AM EDT
To: "gmod-ajax at lists.sourceforge.net" <gmod-ajax at lists.sourceforge.net>
Subject: [Gmod-ajax] Jbrowse on mac os 10.5


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  

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

That would really make my day!



<big rant>
I've spent several hours trying to install Gbrowse on my mac (10.5.6)  
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  
it ;-)

Errors are inconsistent: cpan can't install either LWP, or Harness, or  
or Compress::Zlib. I've first tried to execute the Gbrowse installer  
any options. It crashes with:

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

*** Installing BioPerl ***
Downloading bioperl-live...
Can't locate LWP.pm in @INC (@INC contains:
/System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- 
/Library/Perl/5.8.8 /Library/Perl
/Network/Library/Perl/5.8.8 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/ 
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  

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  
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  
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>

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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