Differences

This shows you the differences between two versions of the page.

--- diy [2009/11/10 06:27] – 172.26.0.166
+++ diy [2009/11/10 06:35] – 172.26.0.166
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 http://sourceforge.net/projects/diyg/
 http://gmod.org/wiki/DIYA
+INSTALLATION
+----
+Get the latest versiont from
+Required Perl modules (available from CPAN)
+        * BioPerl (instructions at http://bioperl.org)
+        * Data::Merger
+        * 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