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README
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README
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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