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https://ctskennerton.github.io/crass/

The CRISPR assembler
https://ctskennerton.github.io/crass/

bioinformatics crispr

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The CRISPR assembler

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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/"