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

Chris Fields cjfields at illinois.edu
Sun Mar 15 11:27:24 EDT 2009

On Mar 15, 2009, at 8:27 AM, Hilmar Lapp wrote:

> 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.)
> 	-hilmar
> 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
> 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 ;-)

On Mac OS X one has to use 'sudo' for installation of anything from  
CPAN unless installing to a location the user has read-write privs to,  
like a local directory.  You can set up BioPerl by just downloading  
it, unpacking the tarball, and adding it to PERL5LIB (that's how I run  

> 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

Appears to be the same issue described above (need to use 'sudo').

> 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

I may test this out and let you know how it goes; will report back  
what I find.


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