obogaf::parser is available on CPAN as well as through Bioconda and also from source code. You can use one of the following ways for installing obogaf::parser.

Installation via Conda

This is the recommended way to install obogaf::parser for normal user because it will enable you to switch software versions easily and in addition Perl with all needed dependencies will be installed.

First, you have to install the Miniconda Python3 distribution. See here for installation instructions. Make sure to …

  • Install the Python 3 version of Miniconda.
  • Answer yes to the question whether conda shall be put into your PATH.

Then, you can install obogaf::parser with

conda install -c bioconda perl-obogaf-parser

from the Bioconda channel.

Global Installation

You can directly install the module via cpan:

$ cpan install obogaf::parser

or via cpanm:

$ cpanm obogaf::parser

make sure to install cpanm before running the command above


to install the obogaf::parser globally you must be a root-user

Local Installation

If you do not have root permit, you can clone (or download) the obogaf::parser git repository (link) and initialize your Perl script as follow:


use strict;
use warnings;
use lib 'path/to/folder/containing/obogaf-parser-module'; ## nb: folder != full filename
use parser;

... beginning of your Perl code ...

Installing from Source

To build obogaf::parser from scratch follow the command shown below:

$ cd ~;
$ git clone git:// obogaf-parser;
$ cd obogaf-parser;

$ perl Makefile.PL;
$ make manifest;
$ make;
$ make test;
$ sudo make install;
$ make veryclean; ## to clean built files


For building obogaf::parser you will need the following dependencies

  • Perl (>= v5.22.1)

  • Perl Module:

    • Graph - graph data structures and algorithms
    • PerlIO::gzip - Perl extension to provide a PerlIO layer to gzip/gunzip
  • Test Module:

    • Test::More - yet another framework for writing test scripts
    • Test::Exception - Test exception-based code
    • Test::Files - A Test::Builder based module to ease testing with files and dirs
  • Configure Module:

    • Module::Metadata - Gather package and POD information from perl module files
    • ExtUtils::MakeMaker - Create a module Makefile