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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 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 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 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:
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>o conf prefer_installer MB
cpan>o conf commit
Now find the name of the bioperl-network version you want:
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
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:
(the instructions are aimed at bioperl-core, but apply
equally to bioperl-network)
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