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

iphan isabelle.phan at sbri.org
Tue Mar 17 20:27:19 EDT 2009


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

</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.

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...

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




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