[Bioperl-l] installing bioperl on an SGI w/freeware perl, gcc, etc.

[Wes Barris]

Can anyone enlighten me on how to install bioperl on an SGI running
IRIX 6.5.18?  I do not have the SGI "cc" compiler.  Instead I have
the freeware versions of gcc-3.2.1, gmake-3.80, perl-5.6.1, etc.

I have modified my /usr/freeware/lib/perl5/5.6.1/irix-n32/Config.pm
file as described here:

http://www.digitalmages.com/irix/#perl

Then, in bioperl-1.2.2, I do this:

perl Makefile.PL

Then I do this:

wes at structure> gmake
gmake: execvp: /bin/sh: Arg list too long
gmake: *** [pm_to_blib] Error 127


If I try using regular make I get this:

wes at structure> make
*** Termination code 138 (bu21)


Here is the full output of running perl Makefile.PL:

wes at structure> perl Makefile.PL
Generated sub tests. go make show_tests to see available subtests

External Module LWP::UserAgent, Part of the LWP package,
  is not installed on this computer.
   The Bio::DB::*,Bio::Tools::Run::RemoteBlast in Bioperl needs it for GenBank+GenPept 
sequence retrieval, remote http Blast jobs

External Module HTTP::Request::Common, Part of the LWP package,
  is not installed on this computer.
   The Bio::DB::*,Bio::Tools::Run::RemoteBlast in Bioperl needs it for GenBank+GenPept 
sequence retrieval, remote http Blast jobs

External Module SOAP::Lite, SOAP protocol,
  is not installed on this computer.
   The Bio::DB::XEMBLService in Bioperl needs it for XEMBL Services (also Bibliographic 
queries in Biblio::)

External Module Text::Shellwords, Execute shell commands,
  is not installed on this computer.
   The Bio::Graphics in Bioperl needs it for test scripts

External Module HTML::Parser, HTML parsing,
  is not installed on this computer.
   The Bio::DB::GDB in Bioperl needs it for HTML parsing of GDB page

External Module DBD::mysql, Mysql driver,
  is not installed on this computer.
   The Bio::DB::GFF in Bioperl needs it for loading and querying of Mysql-based GFF 
feature databases

External Module Ace, Aceperl,
  is not installed on this computer.
   The Bio::DB::Ace in Bioperl needs it for access of ACeDB database

External Module GD, Graphical Drawing Toolkit,
  is not installed on this computer.
   The Bio::Graphics in Bioperl needs it for Rendering Sequences and Features

External Module XML::Twig, Available on CPAN,
  is not installed on this computer.
   The Module Bio::Variation::IO::xml.pm in Bioperl needs it for parsing of XML documents

External Module Storable, Persistent object storage and retrieval,
  is not installed on this computer.
   The Bio::DB::FileCache in Bioperl needs it for Storing sequence objects in local file cache

External Module XML::Parser::PerlSAX, Parsing of XML documents,
  is not installed on this computer.
   The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code, 
GAME parser

External Module XML::Parser, Parsing of XML documents,
  is not installed on this computer.
   The Bio::SeqIO::game,Bio::Variation::* in Bioperl needs it for Bio::Variation code, 
GAME parser

External Module Graph::Directed, Generic Graph data stucture and algorithms,
  is not installed on this computer.
   The Bio::Ontology::SimpleOntologyEngine in Bioperl needs it for Ontology Engine 
implementation for the GO parser


Information:

    There are some external packages and perl modules, listed above, which
    bioperl uses. This only effects the functionality which is listed above:
    the rest of bioperl will work fine, which includes nearly all of the
    core packages.

    The installation of these external packages is very simple. You
    can read more about bioperl external dependencies at

    http://bioperl.org/Core/external.shtml

    Enjoy the rest of bioperl, which you can use after going 'make install'

Writing Makefile for Bio

-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au