AmiGO Manual: Installation: Difference between revisions

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connect to via DBD::mysql (I presume you have this since you have an   
connect to via DBD::mysql (I presume you have this since you have an   
old amigo install).
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=
=Requirements=
Line 119: Line 106:
  XML::Writer;
  XML::Writer;
  YAML;  
  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=
=Example config.pl files=

Revision as of 14:50, 3 April 2008

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.

Stable version

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).

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

Notes

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

Notes

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!