INSTALL

Crumble uses automake and autoconf.

If you have a cloned git repository, run "autoreconf -i" first to
install the necessary files and create the configure script.  This is
not necessary if you downloaded a release tar-ball.

To compile, typically run

    ./configure  [options]
    make

Use "./configure --help" to list the configure options available.

Crumble depends on a pre-compiled htslib.  Preferably this will be
against an installed copy, but it will also work with a sibling
../htslib source tree (which still needs compiling first).

If you have htslib installed in a non-standard location, specify where via

    ./configure --with-htslib=DIR

Note this will not automatically set rpath for you, so you may need to
modify LD_LIBRARY_PATH, DYLD_LIBRARY_PATH or PATH according to your
operating system.  Alternatively if your system supports it RPATH can
be specified at configure time.  For example:

    ./configure --with-htslib=/usr/local LDFLAGS=-Wl,-R/usr/local/lib

This use of LDFLAGS may also be useful when using a sibling ../htslib
directory.