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