This is the PLINK/SEQ repository, to provide the most current
sourcecode for developers of PLINK/SEQ, and additionally for users who
are willing to experiment with the new code (i.e. to try out new
features not yet in the stable release). Please note that this
snapshot comes with absolutly no guarantees as to its stability,
completeness or correctness, and without the offer of any support
besides the (in flux) notes at:

  http://atgu.mgh.harvard.edu/plinkseq/whatisnew.shtml

If you trying to install PLINK/SEQ from source just to run it, you are
almost certainly better off just downloading the source for the latest
stable release from the main website download page:

  http://atgu.mgh.harvard.edu/plinkseq/download.shtml

Typical steps for creating all PLINK/Seq components from source,
assuming certain dependencies are in place (see PREREQUISITES), are
given in the section below.  If any step fails, please refer to the
more detailed description below and to the main website.

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## Obtain source

  git clone https://bitbucket.org/statgen/plinkseq.git

  cd plinkseq

  autoreconf -i


## Make PSEQ (sudo if system-wide installation)

  ./configure

  make

  sudo make install


## Make Rplinkseq (with sudo for system-wide installation)

  cd R/Rplinkseq

  autoreconf -i

  ./configure 

  cd ..

  sudo R CMD INSTALL Rplinkseq 


## Test PSEQ from a command line

  pseq . version
 

## Test Rplinkseq from within R

  library(Rplinkseq)


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** PREREQUISITES ** 

PLINK/SEQ uses GNU Autotools for its 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. Please be sure you
have protobuf version 2.4.1 installed locally:

   http://code.google.com/p/protobuf/


** GETTING THE SOURCE ** 

To clone this repository, run:

   git clone https://bitbucket.org/statgen/plinkseq.git [target dir]


** 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.

The configuration option --enable-debug will stop compiler
optimizations (making code easier to debug and faster to build) and
link pseq as a static binary, without a wrapper shell script.


** Rplinkseq configuration options ** 

To specify the location of libprotobuf, if it is not visible from a system-wide installation, you 
can pass configure arguments with --configure-args. Also, the --library argument can specify where 
the library is installed.  For example:

  R CMD INSTALL Rplinkseq --library=/path/to/R/lib/loc  --configure-args=--with-protobuf=/path/to/protobuf/