Build System

This page describes how to compile the SeqTools package using the Autotools scripts included with the source code.

Autotools

The SeqTools package is configured and built using the GNU Build System (aka Autotools). The relevant configuration files are listed below:

• src/version.m4: This specifies the version number for the build. It is included by configure.ac, which sets the version number in the PACKAGE_VERSION variable in the config.h file, which is included by the code.
• src/configure.ac: This file is processed by autoconf to produce the configure file.
• src/Makefile.am: This file is processed by automake to produce the Makefile.in file.
• src/AUTHORS, src/COPYING, src/README, src/NEWS, src/ChangeLog: These files are for information.
• subdirectory Makefile.am files: The subdirectories blixemApp, dotterApp, seqtoolsUtils and libpfetch all contain a Makefile.am file, which is processed by automake to create a Makefile.in file in that directory.

The build process is as follows:

• Run 'autoreconf -i' in the src directory. This runs autoheader, aclocal, autoconf and automake and creates the configure script (and some other required files) in the src directory.
• cd to the directory where the code is to be built (this can be src or any other directory, e.g. src/build) and run the configure script from there. This will create a makefile in the build directory (and subdirectories for blixemApp, dotterApp, seqtoolsUtils and libpfetch, which all contain a makefile for building that module). It will also create the config.h file that will be included by the code, and a few other required files.
• Run make in the build directory to build everything (or in a subdirectory to build just that module).

Modules

The source code includes the following modules. Each module has its own subdirectory with a makefile that produces a .a convenience library that is statically linked by the executables that require that code. The executables are built by the main Makefile in the src directory. The blixem and blixemh executables both use the same source code (the blixemApp code) but blixemh is compiled using the PFETCH_HTML flag, which conditionally compiles some additional code.

• blixemApp: Blixem application code.
• dotterApp: Dotter application code.
• seqtoolsUtils: Generic utility functions. Required by dotter, blixem and blixemh.
• seqtoolsUtils: Generic seqtools utility functions. Required by dotter, blixem and blixemh.
• libpfetch: Utilities for fetching sequences over http. Required by blixemh.
• gbtools: Generic utility functions from an external repository of shared code. This code is included in the distribution so that it is automatically compiled as part of the seqtools package.

Dependencies

• All of the executables in the SeqTools package require the GLib and GTK+ libraries. These are built using pkg-config. configure.ac specifies which version of the libraries are required.
• blixemh uses the libpfetch library, which requires the libcurl library.
• blixem and blixemh compile in the sqlite3 library if it is availble. If it is not available, the sqlite functionality is disabled.