Jim's installation notes

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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




Comes installed on OS X


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: Downloaded (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

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.

= Set up postgres db for chado

psql postgres