Jim's installation notes
Back to Chado New Users
Contents
Installation on PPC mac
- First do this on my G4 laptop. Then consider whether to install on the XServe.
Installation section of Getting Started describes how to get Chado from CVS. Note, when updating, be sure to be at the directory level just above schema. Getting Started refers to the INSTALL document
Prerequisites
PostgreSQL
- I installed PostgreSQL using the Installer Package from Marc Liyanage
- There are a couple of tools to make working with PostgreSQL easier
- pgAdmin is a GUI desktop app. I have this but haven't figured out how to do anything useful with it.
- phppgadmin web based admin tool analogous to phpmyadmin for mysql
- There are a couple of tools to make working with PostgreSQL easier
Apache
Comes installed on OS X
BioPerl
BioPerl is currently not installed on my laptop, as I ran into the dreaded gd installation problems. Let's try again. Installing BioPerl on Unix applies to Mac OSX once the prereqs are done (I think). Some incomplete notes here from installing on the server. As I recall, this failed the last time I tried on my laptop. However, I think Matías Giovannini updated his Installation guide for gd since the last time I tried it. With the new instructions gd went smoothly. notes here.
GO perl
- The url provided in the Chadon install document is not working for me. Contacted Mike Cherry, who provided an alternative url: http://171.65.76.113/latest-full/. Downloaded http://171.65.76.113/latest-full/go_200703-utilities-src.tar.gz (this URL will change with their next update, use the other to browse the available downloads from the GO consortium).
- go_perl is only one module inside the utilities. From its install docs, there are more CPAN modules to install:
- install GO::Parser
- got this warning:
NOTICE: ** You do not have XML::Parser::PerlSAX installed **
This module is not required for go-perl, but it is required if you wish to parse Obo-XML files. It is also required by the go-db-perl library for loading the GO Database.
If you do not intend to use either Obo-XML or go-db-perl, then you may continue. Even if you do care about these, you may continue and install XML::Parser::PerlSAX at some future time.
- I'm going to need the XML::Parser at some point, I suspect. I recall having problems with this during BioPerl installation. install XML::Parser::PerlSAX follows dependency to install XML::Parser, which complains about not having expat.
- installing expat: get it from http://sourceforge.net/projects/expat/
- install XML::Parser. Note that quitting and restarting CPAN helps if an installation already failed once.
- install XML::Parser::PerlSAX
- install GraphViz - also optional, but likely to be useful
- install GO::Parser
Curiously, the install instructions suggest that this is all I need to do for go_perl. So despite downloading the tarball, all I needed was the CPAN installation??
Other Perl Dependencies
install Bundle::GMOD
As is often the case with the CPAN modules, watching the Terminal window shows lots of tests failing. Also, it looks for modules I'm pretty sure I've already installed.
Failed during this command: GAAS/libwww-perl-5.805.tar.gz : make_test NO MIYAGAWA/Class-DBI-Pager-0.08.tar.gz : make_test NO CAPTTOFU/DBD-mysql-4.003.tar.gz : make_test NO TJMATHER/XML-DOM-1.44.tar.gz : make_test NO JROBINSON/SQL-Translator-0.08.tar.gz : make_test NO TMTM/Class-DBI-v3.0.16.tar.gz : make_test NO ADAMK/AppConfig-1.64.tar.gz : make_test NO ABW/Template-Toolkit-2.18.tar.gz : install NO DMAKI/Class-DBI-Pg-0.08.tar.gz : make_test NO SZABGAB/Spreadsheet-ParseExcel-0.28.tar.gz : make_test NO BYRNE/SOAP-Lite-0.69.tar.gz : make_test NO MIROD/XML-DOM-XPath-0.13.tar.gz : make_test NO
Set up default gmod location
mkdir /usr/local/gmod
Is that it? I don't feel like this is right. Since I installed bundle GMOD using CPAN, I'm not sure where it's gone. Probably /Library/Perl... Forge ahead anyway.
Install chado
A few more prereq issues
perl Makefile.PL ************************************************************************ The following enviroment variables not detected: GMOD_ROOT CHADO_DB_NAME Please read the INSTALL document and set required environment variables. ************************************************************************
Oops. Went back and edited .profile
export GMOD_ROOT="/usr/local/gmod" export CHADO_DB_NAME="chado_trial"
also did these on command line, since .profile settings don't refresh until opening a new Terminal (I think).
perl Makefile.PL
Lots of output. Failed. Possible culprits:
--WARNING------------------------------------------------- The envirnment variable GO_ROOT is not set. Ontology loading may not work correctly without it. ---------------------------------------------------------- Extracting /Users/jimhu/schema/chado/bin/../lib/Chado/AutoDBI.pm (with variable substitutions) Can't locate LWP/Simple.pm in @INC (@INC contains: lib /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level / Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin- thread- multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at lib/Chado/Builder.pm line 15. BEGIN failed--compilation aborted at lib/Chado/Builder.pm line 15. Compilation failed in require at load/Build.PL line 3. BEGIN failed--compilation aborted at load/Build.PL line 3. sh: line 1: ./Build: No such file or directory unable to create Build from load/Build.PL:
Added the line to .profile to set GMOD_ROOT (this was in the install doc and I must have missed it earlier).
export GO_ROOT=$HOME/go-dev
I assume this was set up during install of GO::Parser??
cpan>install LWP::Simple
failed tests. I think these are based on failing to connect to localhost via apache...it may reflect something about OSX that should be set in the config. Try forcing it.
Makefile.pl etc.
Do the Makefile.pl again. End of output is
Warning: the following files are missing in your kit: chado-xml/doc/Chado-XML-overview.asc chado-xml/doc/Chado-XML-overview.html chado-xml/doc/Chado-XML-overview.pdf chado-xml/doc/makefile chaos-xml/doc/chaos-and-chado.html chaos-xml/doc/css/stylesheet.css chaos-xml/index.html modules/cv/doc/deductive_closure.txt Please inform the author. Warning: prerequisite DBIx::DBStag 0.07 not found. Checking if your kit is complete... Looks good Writing Makefile for Bio-Chaos Writing Makefile for gmod -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Makefile written. Now you should do the following, in order: 1. make (creates necessary build files) 2. sudo make install (creates $GMOD_ROOT and subdirectories) -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*WARNING-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* STEP 3 WILL DELETE ANY DATA IN A DATABASE WITH THE DATABASE NAME YOU PROVIDED! -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*WARNING-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* 3. make load_schema (loads SQL schema into database) 4. make prepdb (loads basic data) 5. make ontologies (loads data for various ontologies) Optional Targets: make html (auto-generates html documentation for each module) 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) make clean (remove build related files and ontology tmp dir) make instructions (at any moment display these instructions) -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Followed steps 1-5. Chose to load all the ontologies.
./Build ontologies Available ontologies: [1] Relationship Ontology [2] Sequence Ontology [3] Gene Ontology [4] Chado Feature Properties [5] Cell Ontology [6] Plant Ontology Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4,5,6 fetching files for Relationship Ontology +http://obo.cvs.sourceforge.net/obo/obo/ontology/OBO_REL/relationship.obo?rev=HEAD updated loading...sh: line 1: stag-storenode.pl: command not found System call 'stag-storenode.pl -d 'dbi:Pg:dbname=chado_trial;host=localhost;port=5432' --user jimhu --password lambda tmp/obo/OBO_REL/rel.oboxml' failed: 32512 Died at lib/Chado/Builder.pm line 315, <STDIN> line 1. make: *** [ontologies] Error 2
Back to cpan.
install DBIx::DBStag
failed. Force it. The output during force is more informative. Need to create a role for root in postgres...or is it supposed to work with my username, which has a role? After force, make ontologies seems to work without creating a role for root.
Getting lots of warnings while loading SO. example:
HINT: Use the escape string syntax for backslashes, e.g., E'\\'. WARNING: nonstandard use of \\ in a string literal LINE 1: ... (cvterm_id, value, type_id, rank) VALUES ('222', 'gene\\:<g...
GO is taking a long time...not surprising.