
This is the PLINK/SEQ repository, for developers of PLINK/SEQ only.

If you trying to install PLINK/SEQ from source just to run it, please
download the source code from http://atgu.mgh.harvard.edu/plinkseq/

** PREREQUISITES ** 

PLINK/SEQ uses GNU Autotools for our build system. This is a suite of
tools that generates configuration scripts and
Makefiles. Specifically, the following tools are required:

-- Autoconf 2.61+
-- Automake 1.10+
-- Libtool 2.2+

Please be sure these tools are set up (running, for example, "autoconf
-v" to test your version of Autoconf) before you continue.

PLINK/SEQ also requires Google's Protocol Buffers:
http://code.google.com/p/protobuf/. Please be sure you have protobuf
version 2.4.1 installed locally.


** GETTING THE SOURCE ** 

The source is currently private, so you need to be listed as a
collaborator. 

If you are reading this, presumably you have access to our Github
repository.  The official PLINK/SEQ code is at
http://brettpthomas.github.com/plinkseq.  To clone the repository,
run:

$ git clone git@github.com:brettpthomas/plinkseq.git [target dir]

Before you can get the code, you need to configure Git on your
machine. Github has a good guide here:
http://help.github.com/mac-set-up-git/


** INSTALLATION INSTRUCTIONS ** 

This repository does not contain configure scripts or Makefiles -
rather, it contains the Autotools templates (configure.ac and
Makefile.am) that can be used to generate these files.  As a
developer, you need to generate these files before you can build
PLINK/SEQ. Conveniently, this is one command:

$ autoreconf -i

This will create a bunch of files, including configure scripts and
Makefiles.

After this step is complete, you are ready to build - just follow the
instructions on the website:
http://atgu.mgh.harvard.edu/plinkseq/download.shtml.

Note that while you are developing, you should probably use the
--enable-debug configuration option. This does a couple things:

-- Stops compiler optimizations, which makes code easier to debug and
   speeds up the build

-- Links pseq as a static binary, without a wrapper shell script
