INSTALL

Required Perl modules (available from CPAN)

	* BioPerl (instructions at http://bioperl.org)
	* Data::Merger
	* Getopt::Long
	* FileHandle
	* XML::Simple
	* File::Basename

Linux and Mac OS X users may be able to use yum or fink to install Bioperl.

Suggested software, these are the applications used by the annotation
pipelines in the examples/ directory.

	* Perl 5.8 or greater
	* MUMmer v3.20 		(http://mummer.sourceforge.net/)
	* Glimmer v3.02 	(http://www.cbcb.umd.edu/software/glimmer/)
	* BLAST v2.2.16 	(ftp://ftp.ncbi.nih.gov/blast/)
	* tRNAscan-SE v1.23	(http://lowelab.ucsc.edu/tRNAscan-SE/)
	* Infernal v0.81 	(http://infernal.janelia.org/)
	* rfamscan.pl v0.1	(http://www.sanger.ac.uk/Users/sgj/code/)

Suggested databases, these are the databases and files used by the annotation
pipelines in the examples/ directory.

   * UniRef50				(http://www.ebi.ac.uk/uniref/)
   * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/)

A file called 'Clusters.bcp' is used in one example pipeline, this
file is all the *bcp file in the CLUSTERS directory concatenated together.

The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/.


Install

1. Install all the required Perl modules and any suggested software
   and databases

2. Type the following at a command line

	tar -xvf diya-X.X.X.tar 
	cd diya-X.X.X
	perl Makefile.PL
	make
	make test
	sudo make install

3. Set the $DIYAHOME variable to /path/to/diya-X.X or to wherever you
   would like to see the diya output files.