Setting up the developer environment

This guide will explain how you can create your own local version of any of the Bio2RDF scripts through some worked examples. For this guide, you will need to be familiar with the basics of Git and GitHub as well as running programs from your command line . If this describes you, then read on!

Requirements

• PHP 5.3 or above installed and accessible to your user's PATH
• A local copy of php-lib's:

  git clone https://github.com/micheldumontier/php-lib.git
  

  This command results in:

  Cloning into 'php-lib'...
  remote: Counting objects: 689, done.
  remote: Compressing objects: 100% (327/327), done.
  remote: Total 689 (delta 397), reused 649 (delta 360)
  Receiving objects: 100% (689/689), 176.23 KiB | 0 bytes/s, done.
  Resolving deltas: 100% (397/397), done.
  Checking connectivity... done
  

• A local copy of the Bio2RDF scripts branch:

  git clone --single-branch https://github.com/bio2rdf/bio2rdf-scripts.git
  

  This command should have produced something similar to the following:

  Cloning into 'bio2rdf-scripts'...
  remote: Counting objects: 4464, done.
  remote: Compressing objects: 100% (1995/1995), done.
  remote: Total 4464 (delta 2056), reused 4312 (delta 1916)
  Receiving objects: 100% (4464/4464), 22.08 MiB | 1.02 MiB/s, done.
  Resolving deltas: 100% (2056/2056), done.
  Checking connectivity... done
  

• Bio2RDF scripts require read and write access to local directories to store the source (input) and RDFized (output) files. Prepare the following directory structure somewhere in your computer

  data
    ├── download
    └── rdf
  

  The download directory will contain the source (input) files as downloaded by any of our scripts, while the rdf directory will have the RDF documents generated by our scripts.
• Depending on the script that you wish to run you may need to increase the allowed amount of available RAM to PHP 5. Find the settings file php.ini in your PHP installation and increase the value of the memory_limit parameter. For example:

  #change from this
  memory_limit = 128M
  #to this 
  memory_limit = 1024M
  

Next you'll want to run a parser