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bioperl-network Installation
1. Requirements
2. Installing bioperl-network (Unix or Cygwin)
3. Installing bioperl-network (Windows and ActiveState Perl)
1. Requirements
Perl 5.6.1 is required.
The bioperl-network package depends on the core BioPerl package. See
http://www.bioperl.org/wiki/Getting_BioPerl or the BioPerl INSTALL file
for instructions for downloading and installing BioPerl. You must
install at least the corresponding version of Bioperl: since this
is bioperl-network 1.5.2, bioperl 1.5.2 is required.
bioperl-network also depends on Perl's Graph package. See CPAN at
www.perl.org for instructions on downloading and installing Graph,
use Graph version .80 or greater.
Reading PSI XML files using bioperl-network requires the XML::Twig
module. See CPAN at www.perl.org for instructions on downloading
and installing XML::Twig.
2. Installing bioperl-network (Unix, Mac OS X and Cygwin)
Installation instructions at the following address apply here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
The following sections summarize the essential points from there.
Using CPAN:
To install using CPAN you will need a recent version (v1.8802 has
been tested) of it and your prefer_installer conf set to 'MB':
>cpan
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q
Now find the name of the bioperl-network version you want:
>cpan
cpan>d /bioperl-network/
Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
Distribution S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
Now install:
cpan>install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
If you've installed everything perfectly then you may pass all the tests
run in the './Build test' phase.
It's also possible that you may fail some tests. Possible explanations:
problems with local Perl installation, previously undetected bug in
Bioperl, flawed test script and so on. A few failed tests may not affect
your usage of bioperl-network.
If you decide that the failed tests will not affect how you intend to use
bioperl-network and you'd like to install anyway do:
cpan>force install S/SE/SENDU/bioperl-network-1.5.2_100.tar.gz
This is what most experienced Bioperl users would do. However, if you're
concerned about a failed test and need assistance or advice then contact
bioperl-l@bioperl.org.
Manual installation:
>gunzip bioperl-network-<release-version>.tar.gz
>tar xvf bioperl-network-<release-version>.tar
>cd bioperl-network
where <release-version> is the current release.
>perl Build.PL
You can run regression tests and install bioperl-network using the
following commands:
>./Build test
>./Build install
You may have to have root privileges in order to run './Build install'
successfully on Unix. See the BioPerl INSTALL file for alternative approaches
if you don't have root or administrative privileges.
3. Installing bioperl-network (Windows and ActiveState Perl)
The following page on the BioPerl website has up-to-date
instructions on how to install bioperl-network on Windows:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
(the instructions are aimed at bioperl-core, but apply
equally to bioperl-network)
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