AmiGO Manual: Installation

Overview

AmiGO, at its heart, is a simple perl CGI script. However, behind the simple external interface lies a somewhat baroque system of caches, databases connections, temporary files, and delegation. To set-up all of these things properly, AmiGO provides an installation script ("install.pl") that asks questions about the users environment and tries to catch the biggest errors that one can make during installation, but no program is perfect.

This document is intended to help fill the gap between the cryptic install script and what the developers know because they wrote it.

Download

The developer writing this believes that the easiest way to install AmiGO is just to install it from inside the larger go-dev repository rather than trying to install go-perl and go-db-perl separately.

The first thing that you must do is

Stable version

The most recent stable version should be available from the

Current version

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_RC7.

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).

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; 

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:

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!