diy
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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 | 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:// | ||
http:// | http:// | ||
+ | |||
+ | |||
+ | **INSTALLATION** | ||
+ | |||
+ | ---- | ||
+ | Get the latest versiont from | ||
+ | http:// | ||
+ | |||
+ | Required Perl modules (available from CPAN) | ||
+ | |||
+ | * BioPerl (instructions at http:// | ||
+ | * Data:: | ||
+ | * Getopt:: | ||
+ | * FileHandle | ||
+ | * XML::Simple | ||
+ | * File:: | ||
+ | |||
+ | 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:// | ||
+ | * Glimmer v3.02 | ||
+ | * BLAST v2.2.16 | ||
+ | * tRNAscan-SE v1.23 | ||
+ | * Infernal v0.81 (http:// | ||
+ | * rfamscan.pl v0.1 (http:// | ||
+ | |||
+ | Suggested databases, these are the databases and files used by the annotation | ||
+ | pipelines in the examples/ directory. | ||
+ | |||
+ | * UniRef50 | ||
+ | * Protein Clusters (ftp:// | ||
+ | |||
+ | The file cddid_all.tbl can be found at ftp:// | ||
+ | |||
+ | |||
+ | Quick Install | ||
+ | |||
+ | 1. Install all the required Perl modules and any suggested software and databases | ||
+ | |||
+ | 2. Type the following at a command line | ||
+ | < | ||
+ | cd diya-X.X.X | ||
+ | perl Makefile.PL | ||
+ | make | ||
+ | make test | ||
+ | sudo make install | ||
+ | </ | ||
+ | 3. Set the $DIYAHOME variable to / | ||
+ | < | ||
+ |
diy.txt · Last modified: 2010/05/22 14:19 by 127.0.0.1