Installation

· 64-bit Linux

· Blat v. 34 (http://genome.ucsc.edu/FAQ/FAQblat.html#blat3)

· Velvet 1.0.15 (http://www.ebi.ac.uk/~zerbino/velvet/)

· AMOS (http://sourceforge.net/apps/mediawiki/amos/index.php)

· Vmatch 2.2.4 (http://www.vmatch.de/)

· bwa 0.5.8c (http://bio-bwa.sourceforge.net/)

· MUMmer (http://sourceforge.net/projects/mummer/)

· BioPerl (http://www.bioperl.org)

· Perl modules: Parallel::ForkManager

Optional prerequisites:

· Oases 0.1.18 (http://www.ebi.ac.uk/~zerbino/oases/)

· Bambus 2.33 (http://www.cbcb.umd.edu/software/bambus/)

· Sopra 1.0 (dayarian@physics.rutgers.edu) x1 – x4 scripts

· Ray 2.2.0 (http://denovoassembler.sourceforge.net/)

· Minia 1.6906 (http://minia.genouest.org/)

Required prerequisites:

Installation Steps:

1. Gunzip the file and un-tar the file wherever you want the software to reside.

$ gzip -cd /path/to/Rnnotator-x.x.x.tar.gz | tar xf -

2. Once the installation is finished, move to the Rnnotator-x.x.x/ directory.

$ cd Rnnotator-x.x.x

$ perl Makefile.PL PREFIX=/path/to/installation/dir

$ make && make test && make install

3. All scripts or programs (64-bit binaries for x86_64 chips for Linux) are in the ./scripts

directory. Prior to running Rnnotator, add the scripts directory to the $PATH variable

e.g., PATH=/path/to/Rnnotator/scripts:$PATH

When compiling Velvet and/or Oases it is important to set the CATEGORIES and

MAXKMERLENGTH directives appropriately for your datasets. The CATEGORIES

parameter should be >= the number of libraries types you have. The

MAXKMERLENGTH should be proportionally large enough to cover your read length.

In other words, if the read length is 75, MAXKMERLENGTH should be at least 69, or

so. If you are in doubt, simply set MAXKMERLENGTH to the largest read length when

you are compiling Velvet and Oases.