AmiGO Manual: Installation

Overview

Working...

Download

You need to get the up-to-date source from go-dev/go-perl and go-dev/ go-db-perl (HEAD versions from CVS) and the tagged go-dev/amigo amigo_1_5_RC6.

Current version

The source forge CVS Repository can be found at: geneontology.cvs.sourceforge.net:/cvsroot/geneontology go-dev (this is a change from a couple years ago). I do NOT think you need any subdirectories of go-dev other than go- perl, go-db-perl, or amigo, but you do need a go database you can connect to via DBD::mysql (I presume you have this since you have an old amigo install).

install.pl

Once you have the software, you just go to the amigo directory and type install.pl. You must first set the following ENV variables:

setenv GO_ROOT path_to_go-dev_source_dir setenv PATH /tools/perl/5.8.8/bin:${PATH}:${GO_ROOT}/go-perl/scripts setenv PERLLIB $GO_ROOT/go-perl:$GO_ROOT/go-db-perl:$GO_ROOT/amigo/perl

When you run install.pl it asks you 20 questions about install configuration. The questions are a little cryptic. The first time you run it, it creates a config.pl file. Ours looks like this:

Requirements

General

For sure you need the CPAN Go::TermFinder module, and an up-to-date version of Template::Toolkit (obviously CGI, DBI, and DBD::mysql are mandatory as well, but presumably these are in the old version).

Exhaustive

• Perl version:

• Perl libraries:

AutoSplit;
Bio::DB::SwissProt;
Bio::Index::Swissprot;
Bio::Index::GenBank;
Bio::PrimarySeq;
Bio::SeqIO;
Bio::Species;
Carp;
Config;
CGI;
CGI::Carp;
Data::Dumper;
Data::Stag;
Data::Stag::BaseGenerator;
Data::Stag::SxprWriter;
Data::Stag::Writer;
Data::Stag::XMLWriter;
DBD::mysql;
DBI;
DBIx::DBStag;
DBIx::DBSchema;
Digest::MD5;
DirHandle;
Exporter;
ExtUtils::MakeMaker;
Fcntl;
File::Basename;
File::Find;
File::Temp;
FileHandle;
FreezeThaw;
FindBin;
GD::Graph::pie;
GeneralUtils::XML::Generator;
Getopt::Long;
Getopt::Std;
GO::TermFinder;
GraphViz;
HTML::TableExtract;
HTTP::Cookies;
HTTP::Request;
HTTP::Request::Common;
Inline::C;
IO::Handle;
LWP::Simple;
LWP::UserAgent;
Net::FTP;
Net::SMTP;
Set::Scalar;
Shell;
SQL::Translator;
Storable;
strict;
Template;
Term::ReadLine;
Test;
Text::Balanced;
Tk;
Tk::Label;
Tk::Tree;
Tk::ItemStyle;
utf8;
warnings;
WWW::Mechanize;
XML::Checker;
XML::Checker::Parser;
XML::LibXML;
XML::LibXSLT;
XML::Parser::PerlSAX;
XML::Writer;
YAML; 

Example config.pl files

Be prepared to accept defaults or have an answer for these. Obviously, the path names are the most important.

Example file #1

config.pl

$ENV{GO_ROOT}='/share/goweb/www-data/html/dev';
$ENV{GO_DBNAME}='go';
$ENV{GO_DBHOST}='localhost';
$ENV{GO_DBUSER}='amigo';
$ENV{GO_DBAUTH}='HA YOU DID NOT THINK I WOULD JUST EMAIL THE PASSWORD DID YOU'
$ENV{GO_DBSOCKET}='/db0/mysql/admin/golite/mysql.sock';
$ENV{GO_HAS_COUNT_BY_SPECIES}='1';
$ENV{AMIGO_PROJECT_NAME}='amigo';
$ENV{AMIGO_HTDOCS_PARTIAL_PATH}='/share/goweb/www-data/html';
$ENV{AMIGO_HTDOCS_PARTIAL_URL}='http://amigo.geneontology.org/';
$ENV{AMIGO_CGI_PARTIAL_PATH}='/share/goweb/www-data/cgi-bin';
$ENV{AMIGO_CGI_PARTIAL_URL}='http://amigo.geneontology.org/cgi-bin';
$ENV{AMIGO_SHOW_GP_OPTIONS}='1';
$ENV{AMIGO_SHOW_GRAPHVIZ}='1';
$ENV{AMIGO_DOT_PATH}='/usr/bin/dot';
$ENV{AMIGO_SHOW_BLAST}='1';
$ENV{AMIGO_FASTA_DB}='/share/blast/go-seqdblite.fasta';
$ENV{AMIGO_BLASTP}='/tools/wu-blast/current/blastp';
$ENV{AMIGO_BLASTX}='/tools/wu-blast/current/blastx';
$ENV{AMIGO_BLAST_METHOD}='cgi';
$ENV{AMIGO_QSUB}='/usr/local/command';
$ENV{AMIGO_QUEUE}='/usr/local/queue';
$ENV{AMIGO_PBS_USER}='nobody';
$ENV{AMIGO_MAX_SEQ_NUM}='100';
$ENV{AMIGO_MAX_SEQ_LENGTH}='3000000';
$ENV{AMIGO_SHOW_GOOSE_LINKS}='1';
$ENV{AMIGO_USE_DEFAULT_AMIGO_FILTERS}='1';
$ENV{AMIGO_SHOW_ONT_FILTER}='1';
$ENV{AMIGO_SHOW_TAXID_FILTER}='1';
$ENV{AMIGO_SHOW_SPECIESDB_FILTER}='1';
$ENV{AMIGO_SHOW_EVCODE_FILTER}='1';
$ENV{AMIGO_SHOW_GPTYPE_FILTER}='1';
$ENV{AMIGO_SHOW_ASSBY_FILTER}='0';
$ENV{AMIGO_SHOW_QUAL_FILTER}='0';
$ENV{AMIGO_TEMPLATE_PATHS}='templates/pages:templates/includes';
$ENV{AMIGO_SESSION_DIR}='sessions';
$ENV{AMIGO_MAX_SESSIONS}='200';
$ENV{AMIGO_SESSION_TIMEOUT}='7200';
$ENV{AMIGO_PAGE_SIZE}='50';
$ENV{AMIGO_MAX_RESULTS_HTML}='2000';
$ENV{AMIGO_MAX_RESULTS_DOWNLOAD}='20000';
$ENV{AMIGO_CALCULATE_GP_COUNTS}='0';
$ENV{AMIGO_CALCULATE_TERM_COUNTS}='0';
$ENV{AMIGO_GET_RELEVANCE}='1';
$ENV{AMIGO_CLEVER_MODE}='1';
$ENV{AMIGO_OBSOLETE_BEHAVIOUR}='include_commented';

Example file #2

config.pl

$ENV{GO_ROOT}='/users/sjcarbon/local/src/cvs/go-dev';
$ENV{GO_DBNAME}='go_latest_lite';
$ENV{GO_DBHOST}='spitz';
$ENV{GO_DBUSER}=;
$ENV{GO_DBAUTH}=;
$ENV{GO_DBSOCKET}=;
$ENV{GO_HAS_COUNT_BY_SPECIES}='1';
$ENV{AMIGO_PROJECT_NAME}='amigo';
$ENV{AMIGO_HTDOCS_PARTIAL_PATH}='/www/toy_9012/htdocs';
$ENV{AMIGO_HTDOCS_PARTIAL_URL}='http://toy.lbl.gov:9012';
$ENV{AMIGO_CGI_PARTIAL_PATH}='/www/toy_9012/cgi-bin';
$ENV{AMIGO_CGI_PARTIAL_URL}='http://toy.lbl.gov:9012/cgi-bin';
$ENV{AMIGO_DATA_PATH}='/www/toy_9012/cgi-bin';
$ENV{AMIGO_SHOW_GP_OPTIONS}='1';
$ENV{AMIGO_SHOW_GRAPHVIZ}='1';
$ENV{AMIGO_DOT_PATH}='/usr/bin/dot';
$ENV{AMIGO_SHOW_BLAST}='1';
$ENV{AMIGO_FASTA_DB}='/www/toy_9012/cgi-bin/data/go_20071106-seqdblite.fasta';
$ENV{AMIGO_BLASTP}='/share/bdgp64/wublast/blastp';
$ENV{AMIGO_BLASTX}='/share/bdgp64/wublast/blastx';
$ENV{AMIGO_BLASTN}='/share/bdgp64/wublast/blastn';
$ENV{AMIGO_BLAST_METHOD}='cgi';
$ENV{AMIGO_QSUB}='/usr/local/command';
$ENV{AMIGO_QUEUE}='/usr/local/queue';
$ENV{AMIGO_PBS_USER}='nobody';
$ENV{AMIGO_MAX_SEQ_NUM}='100';
$ENV{AMIGO_MAX_SEQ_LENGTH}='3000000';
$ENV{AMIGO_USE_DEFAULT_AMIGO_FILTERS}='1';
$ENV{AMIGO_SHOW_ONT_FILTER}='1';
$ENV{AMIGO_SHOW_TAXID_FILTER}='1';
$ENV{AMIGO_SHOW_SPECIESDB_FILTER}='1';
$ENV{AMIGO_SHOW_EVCODE_FILTER}='1';
$ENV{AMIGO_SHOW_GPTYPE_FILTER}='1';
$ENV{AMIGO_SHOW_ASSBY_FILTER}='0';
$ENV{AMIGO_SHOW_QUAL_FILTER}='0';
$ENV{AMIGO_TEMPLATE_PATHS}='templates/pages:templates/includes';
$ENV{AMIGO_SESSION_DIR}='sessions';
$ENV{AMIGO_MAX_SESSIONS}='200';
$ENV{AMIGO_SESSION_TIMEOUT}='7200';
$ENV{AMIGO_PAGE_SIZE}='50';
$ENV{AMIGO_MAX_RESULTS_PAGES}='40';
$ENV{AMIGO_CALCULATE_GP_COUNTS}='0';
$ENV{AMIGO_CALCULATE_TERM_COUNTS}='0';
$ENV{AMIGO_GET_RELEVANCE}='1';
$ENV{AMIGO_CLEVER_MODE}='1';
$ENV{AMIGO_OBSOLETE_BEHAVIOUR}='include_commented';

Contacts

If you are still having problems installing the AmiGO software, you can contact the developers directly :

• Seth (sjcarbon) at LBNL (berkeleybop.org)
• gwg () at EBI ()

Good luck

Good luck!