Fan's note 1. required Perl modules ------------------------- All required Perl modules were installed during installation of Chado v1.11 (chado_sgd1). 2. Login as postgres to run the installation. --------------------------------------------- postgres@gen-mac-fan:~/gmod-0.002$ ls -l total 2800 -rw-r--r-- 1 postgres dba 6261 28 Jun 2003 Changes -rw-r--r-- 1 postgres dba 1354005 25 Mar 16:04 Generic-Genome-Browser-1.61.tar.gz -rw-r--r-- 1 postgres dba 10851 26 Mar 14:19 INSTALL -rw-r--r-- 1 postgres dba 3834 26 Mar 16:57 MANIFEST -rw-r--r-- 1 postgres dba 268 4 Dec 18:21 MANIFEST.SKIP -rw-r--r-- 1 postgres dba 671 28 Mar 23:23 META.yml -rw-r--r-- 1 postgres dba 19532 26 Mar 14:19 Makefile.PL -rw-r--r-- 1 postgres dba 3107 26 Mar 14:28 README -rw-r--r-- 1 postgres dba 4245 5 Jan 10:48 README.H_sapiens -rw-r--r-- 1 postgres dba 1315 10 Dec 11:48 README.genbank -rw-r--r-- 1 postgres dba 63 9 Dec 17:16 README.gene_expression -rw-r--r-- 1 postgres dba 3223 26 Mar 15:26 TODO drwxr-xr-x 15 postgres dba 510 28 Mar 23:23 bin/ drwxr-xr-x 10 postgres dba 340 28 Mar 23:23 dat/ drwxr-xr-x 8 postgres dba 272 28 Mar 23:23 doc/ drwxr-xr-x 3 postgres dba 102 28 Mar 23:23 lib/ drwxr-xr-x 7 postgres dba 238 28 Mar 23:23 load/ drwxr-xr-x 19 postgres dba 646 28 Mar 23:23 modules/ drwxr-xr-x 5 postgres dba 170 28 Mar 23:23 src/ 3. Generate makefile --------------------- postgres@gen-mac-fan:~/gmod-0.002$ perl Makefile.PL GMOD_ROOT=/usr/local/gmod CHADO_DB_NAME=chado_sgd2 CHADO_DB_USERNAME=postgres CHADO_DB_PASSWORD=XXX Use the simple install (uses default database schema) [Y] What database server will you be using? [PostgreSQL] What is the Chado database name? [chado_sgd2] What is the database username? [postgres] What is the password for 'postgres'? XXX What is the database host? [localhost] What is your database port? [5432] Where shall downloaded ontologies go? [./tmp] /Users/postgres/tmp Building with the following database options: DBDRIVER=PostgreSQL DBNAME=chado_sgd2 DBUSER=postgres DBPASS=XXX DBHOST=localhost DBPORT=5432 LOCAL_TMP=/Users/postgres/tmp Extracting /Users/postgres/gmod-0.002/bin/../lib/Chado/AutoDBI.pm (with variable substitutions) Checking whether your kit is complete... Looks good initializing load scripts... Creating new 'Build' script for 'Chado' version '0.01' lib/Chado/LoadDBI.pm -> blib/lib/Chado/LoadDBI.pm lib/Chado/Builder.pm -> blib/lib/Chado/Builder.pm lib/Chado/AutoDBI.pm -> blib/lib/Chado/AutoDBI.pm lib/Chado/Config.pm -> blib/lib/Chado/Config.pm Manifying blib/lib/Chado/Builder.pm -> blib/libdoc/Chado::Builder.3 Manifying blib/lib/Chado/Config.pm -> blib/libdoc/Chado::Config.3 Checking if your kit is complete... Looks good Writing Makefile for gmod -=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Makefile written. Now you should do the following, in order: 1. make (creates necessary build files) 2. make load_schema (loads SQL schema into database) NOTE: this will destroy any existing database with the same name as the one you are creating 3. make prepdb (loads basic data) 4. make ontologies (loads data for various ontologies) Optional Targets: make radviews (creates views for gene expression data. this is necessary if you chose expression/rad.sql above) make images (generates images of the schema in several formats) make rm_locks (removes ontology lock files, allowing installation of ontologies on successive builds of the database without removing the ontology files altogether) -=-=-=-=-=-=-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 4. make -------- postgres@gen-mac-fan:~/gmod-0.002$ make /usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" load/bin/genbank2gff3.PLS load/bin/gmod_genbank2gff3.pl cp load/bin/gmod_genbank2gff3.pl blib/script/gmod_genbank2gff3.pl /usr/local/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_genbank2gff3.pl /usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" load/bin/load_ontology.PLS load/bin/gmod_load_ontology.pl cp load/bin/gmod_load_ontology.pl blib/script/gmod_load_ontology.pl /usr/local/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_load_ontology.pl /usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" load/bin/load_gff3.PLS load/bin/gmod_load_gff3.pl cp load/bin/gmod_load_gff3.pl blib/script/gmod_load_gff3.pl /usr/local/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/gmod_load_gff3.pl Manifying blib/man1/gmod_genbank2gff3.pl.1 Manifying blib/man3/Chado::Builder.3 Manifying blib/man1/gmod_load_gff3.pl.1 Manifying blib/man1/gmod_load_ontology.pl.1 Manifying blib/man3/Chado::Config.3 5. make load_schema -------------------- postgres@gen-mac-fan:~/gmod-0.002$ make load_schema /bin/sh /Users/postgres/gmod-0.002/bin/test_load.sh chado_sgd2 Password: dropdb: database removal failed: ERROR: database "chado_sgd2" does not exist Password: CREATE DATABASE Password: database chado_sgd2 created check the info in database "chado_sgd2" postgres@gen-mac-fan:~/gmod-0.002$ psql chado_sgd2 Password: 85 tables chado_sgd2=# \dt List of relations Schema | Name | Type | Owner --------+-----------------------------+-------+---------- public | acquisition | table | postgres public | acquisition_relationship | table | postgres public | acquisitionprop | table | postgres public | analysis | table | postgres public | analysisfeature | table | postgres public | analysisprop | table | postgres public | arraydesign | table | postgres public | arrayprop | table | postgres public | assay | table | postgres public | assay_biomaterial | table | postgres public | assay_project | table | postgres public | assayprop | table | postgres public | author | table | postgres public | biomaterial | table | postgres public | biomaterial_relationship | table | postgres public | biomaterial_treatment | table | postgres public | biomaterialprop | table | postgres public | channel | table | postgres public | contact | table | postgres public | control | table | postgres public | cv | table | postgres public | cvterm | table | postgres public | cvterm_dbxref | table | postgres public | cvterm_relationship | table | postgres public | cvtermpath | table | postgres public | cvtermsynonym | table | postgres public | db | table | postgres public | dbxref | table | postgres public | dbxrefprop | table | postgres public | eimage | table | postgres public | element | table | postgres public | elementresult | table | postgres public | elementresult_relationship | table | postgres public | expression | table | postgres public | expression_cvterm | table | postgres public | expression_image | table | postgres public | expression_pub | table | postgres public | feature | table | postgres public | feature_cvterm | table | postgres public | feature_dbxref | table | postgres public | feature_expression | table | postgres public | feature_gcontext | table | postgres public | feature_pub | table | postgres public | feature_relationship | table | postgres public | feature_synonym | table | postgres public | featureloc | table | postgres public | featuremap | table | postgres public | featuremap_pub | table | postgres public | featurepos | table | postgres public | featureprop | table | postgres public | featureprop_pub | table | postgres public | featurerange | table | postgres public | gcontext | table | postgres public | gcontext_relationship | table | postgres public | gcontextprop | table | postgres public | magedocumentation | table | postgres public | mageml | table | postgres public | organism | table | postgres public | organism_dbxref | table | postgres public | organismprop | table | postgres public | phendesc | table | postgres public | phenstatement | table | postgres public | phenstatement_cvterm | table | postgres public | phenstatement_prop | table | postgres public | phenstatement_relationship | table | postgres public | project | table | postgres public | protocol | table | postgres public | protocolparam | table | postgres public | pub | table | postgres public | pub_author | table | postgres public | pub_dbxref | table | postgres public | pub_relationship | table | postgres public | pubprop | table | postgres public | quantification | table | postgres public | quantification_relationship | table | postgres public | quantificationprop | table | postgres public | study | table | postgres public | study_assay | table | postgres public | studydesign | table | postgres public | studydesignprop | table | postgres public | studyfactor | table | postgres public | studyfactorvalue | table | postgres public | synonym | table | postgres public | tableinfo | table | postgres public | treatment | table | postgres (85 rows) 6. make prepdb --------------- script: /load/etc/initialize.sql fan's note: yeast data are included in the above script in this version load useful data into the following tables: organism contact cvterm pub arraydesign postgres@gen-mac-fan:~/gmod-0.002$ make prepdb ./Build prepdb Password: INSERT 2856401 1 INSERT 2856402 1 INSERT 2856403 1 INSERT 2856404 1 INSERT 2856405 1 INSERT 2856406 1 INSERT 2856407 1 INSERT 2856408 1 INSERT 2856409 1 INSERT 2856410 1 INSERT 2856411 1 INSERT 2856412 1 INSERT 2856413 1 INSERT 2856414 1 INSERT 2856415 1 INSERT 2856416 1 INSERT 2856417 1 INSERT 2856418 1 INSERT 2856419 1 INSERT 2856420 1 INSERT 2856421 1 INSERT 2856422 1 INSERT 2856423 1 INSERT 2856424 1 INSERT 2856425 1 INSERT 2856426 1 INSERT 2856427 1 INSERT 2856428 1 INSERT 2856429 1 INSERT 2856430 1 INSERT 2856431 1 INSERT 2856432 1 INSERT 2856433 1 INSERT 2856434 1 7. make ontologies -------------------- 7.1 test1 ---------- postgres@gen-mac-fan:~/gmod-0.002$ make ontologies Available ontologies: [1] Relationship Ontology [2] Sequence Ontology [3] Gene Ontology [4] Embryonic Mouse Anatomy Ontology [5] Mouse Anatomy Ontology [6] Mouse Pathology Ontology (Pathbase) [7] Cell Ontology Which ontologies would you like to load (Comma delimited)? [0] 3 Which ontologies would you like to load (Comma delimited)? [0] 3 fetching files for Gene Ontology +http://www.geneontology.org/ontology/GO.defs updated +http://www.geneontology.org/ontology/component.ontology updated loading...DBI connect('dbname=chado_sgd2;port=5432;host=localhost','postgres',...) failed: could not connect to server: Connection refused at /usr/local/perl/5.80/Library/Ima/DBI.pm line 316 System call './load/bin/gmod_load_ontology.pl /Users/postgres/tmp/go/component.ontology /Users/postgres/tmp/go/GO.defs' failed: 65280 Died at /Users/postgres/gmod-0.002/lib/Chado/Builder.pm line 285, line 1. make: *** [ontologies] Error 2 7.2 fixing the error -------------------- testing: postgres@gen-mac-fan:~$ psql -h localhost -p 5432 chadodev psql: could not connect to server: Connection refused Is the server running on host "localhost" and accepting TCP/IP connections on port 5432? note: several parameters were changed in $PGDATA/pg_hba.conf and $PGDATA/postgresql.conf. it seems the TCP/IP setting didn't take effect with 'pg_ctl reload" solution: try to shutdown and re-start the server postgres@gen-mac-fan:~/pgsql$ pg_ctl stop waiting for postmaster to shut down.....done postmaster successfully shut down postgres@gen-mac-fan:~/pgsql$ pg_ctl -D $PGDATA -l logfile start postmaster successfully started postgres@gen-mac-fan:~$ psql -h localhost -p 5432 chadodev Password: chadodev=# \ postgres@gen-mac-fan:~$ psql -h gen-mac-fan.princeton.edu -p 5432 chadodev ok! no errors! postgres@gen-mac-fan:~$ perl test4_pg_connection.pl Connected at Wed Mar 31 10:40:03 2004 postgres@gen-mac-fan:~$ perl test_pg_connection.pl Connected at Wed Mar 31 10:40:12 2004 It worked! 7.3 make ontologies (try again!!!) : ----------------------- 3/31/2004 10:42 am - 11 am postgres@gen-mac-fan:~/gmod-0.002$ make ontologies ./Build ontologies Available ontologies: [1] Relationship Ontology [2] Sequence Ontology [3] Gene Ontology [4] Embryonic Mouse Anatomy Ontology [5] Mouse Anatomy Ontology [6] Mouse Pathology Ontology (Pathbase) [7] Cell Ontology Which ontologies would you like to load (Comma delimited)? [0] 3 fetching files for Gene Ontology +http://www.geneontology.org/ontology/GO.defs updated +http://www.geneontology.org/ontology/component.ontology updated loading...done! +http://www.geneontology.org/ontology/function.ontology updated loading...done! +http://www.geneontology.org/ontology/process.ontology updated loading...done! 8. make install ---------------- postgres@gen-mac-fan:~/gmod-0.002$ sudo make install password: Installing /usr/local/perl/5.80/Library/Chado/AutoDBI.pm Installing /usr/local/perl/5.80/Library/Chado/LoadDBI.pm Installing /usr/local/perl/5.80/man/man1/gmod_genbank2gff3.pl.1 Installing /usr/local/perl/5.80/man/man1/gmod_load_gff3.pl.1 Installing /usr/local/perl/5.80/man/man1/gmod_load_ontology.pl.1 Installing /usr/local/perl/5.80/bin/gmod_load_gff3.pl Writing /usr/local/perl/5.80/Library/darwin/auto/gmod/.packlist Appending installation info to /usr/local/perl/5.80/Library/darwin/perllocal.pod