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A fast multi-threaded k-mer counter
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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. 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 devellopped 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/>.