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

[Toshiaki Katayama]

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
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> 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)
> -----------------------------------------------------
>
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