Installation¶
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
Note
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:
#!/usr/bin/perl
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://github.com/marconotaro/obogaf-parser.git obogaf-parser;
$ cd obogaf-parser;
$ perl Makefile.PL;
$ make manifest;
$ make;
$ make test;
$ sudo make install;
$ make veryclean; ## to clean built files
Dependencies¶
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