Installation
============

% ./configure
% make
# As root:
% make install

To install in a custom directory:

% ./configure --prefix=/my/dir
% make
% make install

Then make sure the following environment variables contain the correct
paths:

PATH            -> /my/dir/bin
LD_LIBRARY_PATH -> /my/dir/lib
MANPATH         -> /my/dir/share/man
PKG_CONFIG_PATH -> /my/dir/lib/pkgconfig

Only the PATH environment variables is necessary to run
jellyfish. MANPATH is used by the man command. PKG_CONFIG_PATH and
LD_LIBRARY_PATH are used to compile software against the jellyfish
shared library.

GCC requirement
===============

GCC version 4.4 or higher is required to compile Jellyfish. Most
current Linux distribution provides a version of gcc current
enough. On RedHat 5.x, install the packages gcc44 and gcc44-c++.

To install on Mac OS X: Jellyfish 2.0 does not compile with Apple's
Xcode GCC 4.2. Instead, the easiest thing to do is to install GCC 4.8
using MacPorts (http://www.macports.org) using the following commands:

        sudo port install gcc48
        sudo port install gcc_select
        sudo port select -set gcc mp-gcc48

The first command installs GCC version 4.8. The third command makes
that version of GCC the default, and the second installs a package that
makes the third command work. After the above, you should be able to
run './configure ; make' as normal.

Tests
=====

To run the built-in tests, do:

% make check

All tests should pass and 1 test should be skipped (big.sh). Running
'make check' will use about 50MB of disk space and will use every CPUs
found on the machine. On our test machine with 32 cores, it takes a
few minutes to run.

To tests also on large data set, do:

% make check BIG=1

WARNING: this uses >40GB of disk space and takes 30 minutes to run (20
to create the data, 10 to run jellyfish).

Notes
=====

* Jellyfish has been developed and tested on x86-64 GNU/Linux. It
  compiles and runs correctly the tests on MacOS X (Intel) and
  FreeBSD. It should be fairly easy to port on other *NIX platform
  with the gcc compiler, but no guarantee is made. Support for 32-bits
  platform has not been tested.

License
=======

* The Mersenne Twister random generator is copyrighted by Agner Fog
  and distributed under the GPL version 3 or
  higher. http://www.agner.org.

* The Half float implementation is copyrighted by Industrial Light &
  Magic and is distributed under the license described in the
  HalfLICENSE file.

*   This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.