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doc/H03-May-2022-648634

include/jellyfish/H05-Feb-2020-10,7337,318

jellyfish/H05-Feb-2020-2,0281,543

lib/H03-May-2022-5,1504,052

m4/H05-Feb-2020-10,4339,468

sub_commands/H05-Feb-2020-6,6095,846

swig/H05-Feb-2020-19,09514,835

tests/H05-Feb-2020-467303

unit_tests/H05-Feb-2020-33,54722,295

LICENSE-BSD-3-ClauseH A D13-Jul-20191.5 KiB3024

LICENSE-GPL-3.0H A D13-Jul-201934.3 KiB675553

Makefile.amH A D05-Feb-20209.6 KiB231179

Makefile.inH A D05-Feb-2020172.7 KiB2,8672,584

READMEH A D13-Jul-20192.4 KiB8661

aclocal.m4H A D23-Aug-201996.8 KiB2,6032,437

compat.sh.inH A D13-Jul-2019627 3025

compileH A D23-Aug-20197.2 KiB348258

config.guessH A D23-Aug-201943.2 KiB1,4811,288

config.h.inH A D23-Aug-20195.1 KiB198132

config.rpathH A D28-Mar-201814.6 KiB546438

config.subH A D23-Aug-201935.3 KiB1,8021,661

configureH A D23-Aug-2019654.8 KiB21,42718,219

configure.acH A D13-Jul-20196.9 KiB167145

depcompH A D23-Aug-201923 KiB792502

gtest.mkH A D13-Jul-2019588 1910

install-shH A D23-Aug-201914.8 KiB509329

jellyfish-2.0.pc.inH A D28-Mar-2018278 119

ltmain.shH A D23-Aug-2019316.8 KiB11,1577,986

missingH A D23-Aug-20196.7 KiB216143

test-driverH A D23-Aug-20194.5 KiB14987

README

1Installation
2============
3
4% ./configure
5% make
6# As root:
7% make install
8
9To install in a custom directory:
10
11% ./configure --prefix=/my/dir
12% make
13% make install
14
15Then make sure the following environment variables contain the correct
16paths:
17
18PATH            -> /my/dir/bin
19MANPATH         -> /my/dir/share/man
20PKG_CONFIG_PATH -> /my/dir/lib/pkgconfig
21
22Only the PATH environment variables is necessary to run
23jellyfish. MANPATH is used by the man command. PKG_CONFIG_PATH is used
24to compile software against the jellyfish shared library.
25
26GCC requirement
27===============
28
29GCC version 4.4 or higher is required to compile Jellyfish. Most
30current Linux distribution provides a version of gcc current
31enough. On RedHat 5.x, install the packages gcc44 and gcc44-c++.
32
33To install on Mac OS X: Jellyfish 2.0 does not compile with Apple's
34Xcode GCC 4.2. Instead, the easiest thing to do is to install GCC 4.8
35using MacPorts (http://www.macports.org) using the following commands:
36
37        sudo port install gcc48
38        sudo port install gcc_select
39        sudo port select -set gcc mp-gcc48
40
41The first command installs GCC version 4.8. The third command makes
42that version of GCC the default, and the second installs a package that
43makes the third command work. After the above, you should be able to
44run './configure ; make' as normal.
45
46Tests
47=====
48
49To run the built-in tests, do:
50
51% make check
52
53All tests should pass and 1 test should be skipped (big.sh). Running
54'make check' will use about 50MB of disk space and will use every CPUs
55found on the machine. On our test machine with 32 cores, it takes a
56few minutes to run.
57
58To tests also on large data set, do:
59
60% make check BIG=1
61
62WARNING: this uses >40GB of disk space and takes 30 minutes to run (20
63to create the data, 10 to run jellyfish).
64
65Notes
66=====
67
68* Jellyfish has been developed and tested on x86-64 GNU/Linux. It
69  compiles and runs correctly the tests on MacOS X (Intel) and
70  FreeBSD. It should be fairly easy to port on other *NIX platform
71  with the gcc compiler, but no guarantee is made. Support for 32-bits
72  platform has not been tested.
73
74License
75=======
76
77* The Mersenne Twister random generator is copyrighted by Agner Fog
78  and distributed under the GPL version 3 or
79  higher. http://www.agner.org.
80
81* The Half float implementation is copyrighted by Industrial Light &
82  Magic and is distributed under the license described in the
83  HalfLICENSE file.
84
85* This software is dual licenced. See LICENSE file.
86