Developer setup

Most important thing to do is to set the corrent python and perl path. The "env.sh" script can be evaluated to set it correctly:

$ eval $(./env.sh)

Directory structure:

doc

Documentation files under SVN control.

src

Sources.

src/perl

Perl sources.

src/perl/cls

Sources providing classes, no shell commands though.

src/perl/cmd

Sources providing shell commands (applying classes).

src/perl/utest

Unit test framework for Perl API

src/python

Python sources

src/python/cls

Sources providing classes, no shell commands though.

src/python/cmd

Sources providing shell commands applying classes.

src/python/common

Important settings on a global scale. Of interest/use for all modules.

src/python/utest

Unit test framework for Python API

src/utest

Shared functions between the unit tests.

html

This is the documentation directory generated by Doxygen. (NOT under svn)

data

Data directory. This is a link or a mirror of the actual data dir.

galaxy

Galaxy XML tool definition files and installation programs.

Main project Makefile

A Makefile is present root folder of the project. Currently it has the following targets:

• make doc : regenerates all project documentation into html
• make check : run all the test suites (Python and Perl). Please note: the environment must be already set-up.
• make clean : remove temporary files created by Python and the test suite.

EnsEMBL API installation

"DataIntegrator.cfg" expects the EnsEMBL API to be installed in a certain way, so that all the EnsEMBL API versions can be available at the same time, depending on the user's choice.

prefix/

The API prefix, as specified in "DataIntegrator.cfg".

prefix/bin/

Required binaries (such as calc_genotypes)

prefix/lib/site_perl/

Installation root of the Perl API. Put all the Perl API source (core, variation, etc) in this directory.

See Compiling C programs for Ensembl API for some details on compiling the small API C programs.