Differences

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--- diy [2009/11/10 06:27] – 172.26.0.166
+++ diy [2010/05/22 14:19] (current) – external edit 127.0.0.1
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-**DIYA**
+**DIYA:: (currently works on HPC head node only)**
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 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://sourceforge.net/projects/diyg/
 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
+. Install all the required Perl modules and any suggested software and databases
+. Type the following at a command line
+<code>tar -xvf diya-X.X.X.tar
+        cd diya-X.X.X
+        perl Makefile.PL
+        make
+        make test
+        sudo make install
+</code>
+. Set the $DIYAHOME variable to /path/to/diya-X.X or to wherever you would like to see the diya output files.