DIYA - Do It Yourself Annotator

Diya is software that runs sequence annotation pipelines, it is
part of the Do It Yourself Genomics (DIYG) bioinformatics project
community at http://sourceforge.net/projects/diyg.

Copyright (C) 2008 Navy Medical Research Center

The contributors hold the copyright to this work, and it is licensed
under the terms of the GNU General Public License, version 3 or later
(see http://www.gnu.org/licenses/gpl.txt). Derivative works and later
versions of the code must be free software licensed under the same
terms.

THIS REPOSITORY

The files in the diya/trunk directory from diyg.sourceforge.net were
used to make this repository.

INSTALLATION

For software requirements and installation details see the INSTALL file.

DOCUMENTATION

See the file docs/diya.html or read the documentation in diya.pm.
One way to do this is:

 >perldoc diya

This will work if you've run 'make install'and Perl knows where to
find diya. Alternatively:

 >perldoc lib/diya.pm

Or wherever diya.pm can be found.

SAMPLE PIPELINES

Diya is not itself a pipeline, but rather a simple infrastructure for running
pipelines which take the form of xml configuration files.  Several sample 
pipelines are provided under the /examples directory.  Some of these includes...

genome-annotator.conf		- annotate 454 assemblies for NCBI submission
genome-annotator-fasta.conf - annotate sequences in plain fasta format
download-and-annotate.conf	- download from ncbi, run basic glimmer annotations
download-and-format.conf	- download from ncbi, generate blast targets

There are also several single-step .conf files names after individual diya parser
modules.


FREQUENTLY ASKED QUESTIONS

Q:	What is the Clusters.bcp file and where can I find it?

A:	It's basically an index of all the clusters found in the NCBI protein 
	clusters database.


Q:	I'm getting an error from rnammer along the lines of "FATAL: POSIX threads 
	support is not compiled into HMMER; --cpu doesn't have any effect".  What do
	I do?
	
A: This error is basically caused by sending the --cpu option to hmmsearch, 
	which is called in the core-rnammer script.  A quick remedy is to remove it 
	from the script file.  It should be on lines 114 and 187 (make sure to get 
	both!).

	Optionally you can run the following from a command line..
		% perl -pi -e "s/\-\-cpu 1//g\" /path/to/core-rnammer