DIYA:: (currently works on HPC head node only)

DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline framework, written in Perl, used for the rapid annotation of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence.

DIYA is intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

http://gmod.org/wiki/DIYA

INSTALLATION

Get the latest versiont from http://sourceforge.net/projects/diyg/

Required Perl modules (available from CPAN)

• BioPerl (instructions at http://bioperl.org)
• Data::Merger (I had problems installing Data::merger from CPAN console so I downloaded the source "Data utilities" http://search.cpan.org/~cornelis/Data-Utilities-0.04/ and compiled manually)
• Getopt::Long
• FileHandle
• XML::Simple
• File::Basename

Linux and Mac OS X users should 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/)

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

Quick 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.