AmiGO Manual: Installation: Difference between revisions
No edit summary |
No edit summary |
||
Line 20: | Line 20: | ||
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). | ||
=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!