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

[Davide Rambaldi]

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.
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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)
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