[BioRuby] Installation from git repository on a MAC Intel 10.5.5
Davide Rambaldi
davide.rambaldi at ifom-ieo-campus.it
Wed Oct 15 10:26:44 UTC 2008
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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