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crass -- CRisprASSembler -- version 1 subversion 0 revision 0 (1.0.1) ======================================================================= CITATION -------- Connor T. Skennerton, Michael Imelfort, and Gene W. Tyson Crass: identification and reconstruction of CRISPR from unassembled metagenomic data Nucl. Acids Res. (2013) 41(10): e105 COPYRIGHT --------- Copyright 2011-2015 Connor Skennerton & Michael Imelfort. All rights reserved. Copyright 2016 Connor Skennerton. All rights reserved. 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 . CONTRIBUTED CODE ---------------- crass would not have been possible without the code found freely available at the following locations: [Boyer-Moore Search Algorithm](http://dev-faqs.blogspot.com/2010/05/boyer-moore-algorithm.html) [Aho-Corasick Search Algorithm](https://github.com/mischasan/aho-corasick) [Levensthein String Comparison Algorithm](http://www.merriampark.com/ldcpp.htm) [CRISPR Recognition Tool (CRT)](http://www.room220.com/crt) [SaSSY - Short read assembler](http://sassy.mikeimelfort.com) [klib](http://github.com/attractivechaos/klib) - For kseq & ksw code INSTALLATION ------------ Crass requires a UNIX operating system and has been tested on 64-bit Linux personal computers with intel processors and servers with 64-bit Opteron processors. It successfully compiles with gcc 4.4.5 and gcc 4.6.3 other versions of gcc have not been tested. Crass requires [Xerces-c](http://xerces.apache.org/) version 3.1.1 and [Zlib](www.zlib.net) to be installed for compilation. Optionally you can also install the [Graphviz package](www.graphviz.org) for rendering graphs. WARNING: Do not install the binary distribution of Xerces from their website, it is broken and looks for other shared libraries in specific places. Install xerces from source or using a package manager for you system. With all this in mind to perform the installation: download the source files from git. then on most Unix systems: $ tar -xf crass.tar.gz $ cd crass $ ./autogen.sh $ ./configure $ make $ make install NON-STANDARD INSTALLATIONS -------------------------- Crass can access the graphviz libraies and executables if desired. Use the `--enable-rendering` during configure to access this feature. If Xerces is installed in a non-standard loacation use the `--with-xerces=[PREFIX]` configure option to change the location prefix. Configure will look for `$prefix/lib/` and `$prefix/include` directories for the library objects and header files. Note that the below options for changing `LDFLAGS` and `CPPFLAGS` will not work for Xerces as it is a C++ library and not a C library and therefore different code is used to check for it. `LDFLAGS` - set this environmental variable during configure to add to the path where library object files can be found. Don't forget to use `-L` a the begining `CPPFLAGS` - set this environmental variable during configure to add to the path where header files are located. example: $ ./configure --enable-rendering LDFLAGS="-L/usr/home/user_name/local/lib/" CPPFLAGS="-I/usr/home/user_name/local/include/"

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