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.