[Bioperl-l] Problem installing CJFIELDS/BioPerl-1.6.1.tar.gz

[pablo marin-garcia]

On Fri, Feb 4, 2011 at 1:20 PM, Chad Davis <chad.a.davis at gmail.com> wrote:
> I may be off track here, but I saw a reference to GraphViz (though no
> specific error) above. This reminded me of many problems I've had with
> the GraphViz module over the last several years, though I think it's
> better today. I generally had to, in CPAN:
>
> force install GraphViz
>
> before installing BioPerl. Make sure you have graphviz installed, first:
>

Hello Chad,

Regarding GraphViz and other dependencies when installing bioperl and
biographics [now independent of bioperl]
I wrote a description of my problem that I have before here
http://pablomarin-garcia.blogspot.com/2010/04/installing-graphviz-from-perl-cpan.html
http://pablomarin-garcia.blogspot.com/2010/04/perl-biographics-module-dependencies-in.html

In the case of GraphViz it needs
"Warning: prerequisite IPC::Run 0.6 not found."

What I needed for installing it in a new ubuntu 9.04 box:  (in a mac
would be different)
[Note the following dependencies could not be for bioperl but for
biographics or both, but it is nice to have them anyway]
[ sudo aptitude install]
- libgd2-xpm-dev # gd for GD. I don't know the difference between xpm
and noxpm but anyway
- libexpat-dev # expat for XML::Parser
- graphviz graphviz-dev graphviz-doc libgraphviz-dev graphviz-cairo #
for GraphViz
- libdb4.6-dev # for DB_File (The headers for 4.7 were also available
but I had 4.6 installed)

[CPAN]
- install IPC::Run # for GraphViz and other modules
- install DB_File # used by several modules so it better to install it first
- install XML::parser
- install GraphViz
- install GD
- install CJFIELDS/BioPerl-1.6.1.tar.gz

The only caveats here were that you should know that you need the
expat for XML, IPC::Run for GraphViz dependency and that DB_File uses
the Berkeley db headers (that I needed to google for finding the
package that contains them).



-- 
   - Pablo Marin-Garcia