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The Stacks Pipeline
-------------------

0. Prerequisites

Stacks should build on any standard UNIX-like environment (Apple OS X, Linux, 
etc.) Stacks is an independent pipeline and can be run without any additional
external software. 

If compiling with the standard GCC compiler, Stacks needs a version of the compiler
newer than GCC 4.9.0.

1. Build the software. Stacks uses the standard autotools install:

% tar xfvz stacks-x.xx.tar.gz
% cd stacks-x.xx
% ./configure

You can change the root of the install location (/usr/local/ on most
operating systems) by specifying the --prefix command line option to
the configure script.

% ./configure --prefix=/home/smith/local

You can enable Sparsehash by adding the following options:

% ./configure --enable-sparsehash

% make

You can speed up the build if you have more than one processor:

% make -j 8

3. Install the software.

% sudo make install

A default Stacks install will install files in the following way:

/usr/local/bin - stacks executables and perl scripts

The pipeline is now ready to run.