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

Chris Fields cjfields at illinois.edu
Tue Mar 17 23:30:53 EDT 2009

On Mar 17, 2009, at 7:27 PM, iphan wrote:

> On 3/15/09 11:27 AM, "Chris Fields" <cjfields at illinois.edu> wrote:
>> 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
>> it).
> If it is that simple, then it would help immensely if the INSTALL
> instruction would be updated, because the latest release says:
> <bioperl-instruction>
> Download, then unpack the tar file. For example:
>> gunzip bioperl-1.5.2_100.tar.gz
>> tar xvf bioperl-1.5.2_100.tar
>> cd bioperl-1.5.2_100
> Now issue the build commands:
>> perl Build.PL
>> ./Build test
> <blurb/>
>> ./Build install

The following, from the INSTALL file, alludes to the use of 'sudo' but  
could be made clearer:

"To './Build install' you need write permission in the
perl5/site_perl/source area (or similar, depending on your
environment). Usually this will require you becoming root, so you will
want to talk to your systems manager if you don't have the necessary

> </bioperl-instruction>
> I've followed the instructions, ran cpan as 'sudo' and could not get  
> past
> the required libraries:
>    HTML::Tagset
>    Digest::MD5
> Cpan crashes trying to install these, returns to BioPerl libraries,  
> fails,
> and we are back to the beginning: cpan asks for installation of  
> HTML::Tagset
> and Digest::MD5, and enters an infinite loop of endlessly crashing  
> installs.

It's hard to narrow down the problem w/o some actual output.  Can you  
send output that the installation is producing?

The infinite loop is particularly worrisome; I'm assuming that stems  
from the automated CPAN installation within Bio::Root::Build module.   
If this is true my inclination is to turn that functionality off (or  
at least make it optional) until the problem is resolved; it's a  
definite bug.

Just to note: the two above packages you are having problems with are  
not direct requirements for BioPerl 1.6 (aren't listed in Build.PL nor  
in DEPENDENCIES).  That's not to say they aren't somewhere in the  
dependency tree, however.

> I had assumed one HAD to run the build in order to resolve all the
> dependencies. Going through the DEPENDENCIES document is not really  
> helpful,
> because a) you are warned that the list is not complete, and b) you  
> realize
> the actual length of the list of dependencies is depressingly long...

You can run Build.PL directly and it will attempt to check  
dependencies (required and recommended dependencies are listed in the  
Build.PL file).  We do NOT require you to install everything, hence  
the division between  'required' vs 'recommends', the former required  
for the most critical core classes.  The 'recommends' modules are only  
useful if you want full functionality, and my guess is you will never  
use every single module in BioPerl's core modules.

For Gbrowse functionality, you would need some minimal stuff (GD for  
Bio::Graphics, Text::Parsewords, and maybe one or two more).  I'm not  
sure what you would need for JBrowse, you would need to ask the devs  
for that.

> I am aware of the heroic efforts of the GMOD people to distribute  
> virtual
> machines with everything prepackaged, but somehow I wonder if this  
> is a
> sustainable solution to the Perl dependency issue?
> Isabelle

Sorry that you're having problems with the installation.  You are more  
than welcome to file a bug in bugzilla:



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