[BioRuby] Installation from git repository on a MAC Intel 10.5.5

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Sun Oct 19 05:15:10 UTC 2008


Hi,

I get the setup.rb from Minero Aoki's svn repository
(see http://i.loveruby.net/en/projects/setup/ for details),
and replace install.rb with this newest setup.rb.
README.rdoc is also modified.

http://github.com/bioruby/bioruby/commit/9def7df5b81340c49534ff0bb932de62402a1c8d

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 16 Oct 2008 09:49:54 +0900
Toshiaki Katayama <ktym at hgc.jp> wrote:

> Hi,
> 
> > - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
> >
> > - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
> 
> install.rb in the BioRuby package is a old version of the setup (3.1.4)
> >From your experiment, we should update it to the version 3.41. Thanks!
> 
> bioruby/README:
> --------------------------------------------------
> == LICENSE
> 
> BioRuby can be freely distributed under the same terms as Ruby.
> 
> Note that, install.rb included in the BioRuby package comes from
> setup[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki,
> and modified by Moses Hohman.
> --------------------------------------------------
> 
> bioruby/ChangeLog:
> --------------------------------------------------
> 2004-12-13  KATAYAMA Toshiaki <k at bioruby.org>
> 
>         * BioRuby 0.6.2 released.
> 
>         * test/all_tests.rb:
> 
>           Unit tests for some classes are newly incorporated by
>           Moses Hohman.  You can try it by 'ruby install.rb test'
> 
> 2003-06-25  KATAYAMA Toshiaki  <k at bioruby.org>
> 
>         * BioRuby version 0.5.0 released.
> 
>         * install.rb:
> 
>             Changed to use setup 3.1.4 to avoid installing CVS/ directory.
> --------------------------------------------------
> 
> Regards,
> Toshiaki Katayama
> 
> 
> On 2008/10/15, at 19:26, Davide Rambaldi wrote:
> 
> > About the installation of bioruby on a fresh MAC 10.5
> >
> > I manage to install it in the correct path without install ruby in /usr/local/bin
> >
> > Here is the story:
> >
> > - I get the last version of RAA: setup from http://raa.ruby-lang.org/project/setup/  (setup-3.41.tar.gz)
> >
> > - I just copy setup.rb in the bioruby directory (I still doesn't understand who generate install.rb for bioruby, is autogenerated I see, but with which ruby package?)
> >
> > - I use the setup.rb file:
> >
> >   * ruby setup.rb config
> >   * ruby setup.rb setup
> >
> > At this point this is the config I have:
> >
> > ruby setup.rb show
> >
> > prefix               /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> > bindir               $prefix/bin
> > libdir               $prefix/lib
> > datadir              $prefix/share
> > mandir               /usr/share/man
> > sysconfdir           $prefix/etc
> > localstatedir        $prefix/var
> > libruby              /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby
> > librubyver           /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8
> > librubyverarch       /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0
> > siteruby             /Library/Ruby/Site
> > siterubyver          /Library/Ruby/Site/1.8
> > siterubyverarch      /Library/Ruby/Site/1.8/universal-darwin9.0
> > rbdir                $siterubyver
> > sodir                $siterubyverarch
> > rubypath             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > rubyprog             /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > makeprog             make
> > shebang              ruby
> > without-ext          no
> >
> >
> >
> > That compared with the config saved by install.rb is really different (the critical point id the siteruby path, that is in /Library/Ruby...):
> >
> > ruby install.rb show
> > prefix     /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr
> > std-ruby   $prefix/lib/ruby/1.8
> > site-ruby-common (not specified)
> > site-ruby  (not specified)
> > bin-dir    $prefix/bin
> > rb-dir     $site-ruby
> > so-dir     (not specified)
> > data-dir   $prefix/share
> > ruby-path  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > ruby-prog  /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
> > make-prog  make
> > without-ext no
> >
> >
> >
> > Now I can run sudo ruby setup.rb install  (or ruby setup.rb install --no-harm for just checking):
> >
> > And the installation goes more or less well:
> >
> > - all the lib files are installed into /Library/Ruby/Site/1.8
> >
> > - the binary are installed in /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin
> >
> > So remains to do a post-install command to generate a link from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/bioruby to /usrbin/bioruby ....
> >
> >
> > END of the story.....
> >
> >
> > I will compile my personal ruby in /usr/local/bin amd renstall bioruby in any case: I have seen problems also with the rubygem update, etc....  :-(
> >
> >
> >
> >
> > Davide Rambaldi, Bioinformatics PhD student.
> > -----------------------------------------------------
> > Bioinformatic Group IFOM-IEO Campus
> > Via Adamello 16, Milano
> > I-20139 Italy
> > [t] +39 02574303 066
> > [e] davide.rambaldi at ifom-ieo-campus.it <mailto:davide.rambaldi at ifom-ieo-campus.it>
> > [i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi <%20http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi> (homepage)
> > [i] http://www.semm.it <http://www.semm.it/>             (PhD school)
> > [i] http://www.btbs.unimib.it/     (Master)
> > -----------------------------------------------------
> >
> > _______________________________________________
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> 
> 
> 
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