Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/libs/rubymods
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv19430
Added Files:
bioruby-rb.info bioruby-rb.patch
Log Message:
new pkg bioruby-rb 1.4.3.0001
--- NEW FILE: bioruby-rb.info ---
Info2: <<
Package: bioruby-rb%type_pkg[ruby]
Version: 1.4.3.0001
Revision: 1
Type: ruby (1.9 2.0)
Description: Open source bioinformatics library for Ruby
License: GPL
Maintainer: None <fink-de...@lists.sourceforge.net>
# Dependencies:
Depends: <<
ruby%type_pkg[ruby]
<<
BuildDepends: <<
ruby%type_pkg[ruby]-dev
<<
Recommends: <<
hmmer,
mafft,
muscle,
tcoffee
<<
Suggests: <<
clustalw2,
emboss
<<
# Unpack Phase:
Source: http://bioruby.org/archive/bioruby-%v.tar.gz
Source-MD5: 309c17622f827501bc7f10d8b1c284a7
Source-Checksum: SHA1(aa9941d0b11da4b28b4054c25c624d7a70624c2e)
PatchFile: %{ni}.patch
PatchFile-MD5: da9700d0c38f509f8f6665e750fac3a3
PatchScript: <<
%{default_script}
### make samples have the correct shebang
perl -pi -e 's|!/usr/bin/env ruby|!%p/bin/ruby%type_raw[ruby]|g'
sample/*.rb
perl -pi -e
's|!/usr/proj/bioruby/bin/ruby|!%p/bin/ruby%type_raw[ruby]|g' sample/biofetch.rb
<<
# Compile Phase:
CompileScript: <<
%p/bin/ruby%type_raw[ruby] setup.rb config
%p/bin/ruby%type_raw[ruby] setup.rb setup
<<
InfoTest: <<
TestDepends: <<
libxml2-rb%type_pkg[ruby]
<<
TestScript: <<
#!/bin/sh -ev
%p/bin/ruby%type_raw[ruby] test/runner.rb || exit 2
<<
<<
# Install Phase:
InstallScript: <<
#!/bin/sh -ev
%p/bin/ruby%type_raw[ruby] setup.rb install --prefix=%d
mkdir -p %i/share/%n/sample
cp -R sample/ %i/share/%n/sample
### prepare for u-a
for file in %i/bin/*; do
mv $file $file-rb20
done
<<
PostInstScript: <<
update-alternatives --install %p/bin/bioruby bioruby
%p/bin/bioruby-rb%type_pkg[ruby] %type_pkg[ruby] \
--slave %p/bin/br_biofetch br_biofetch
%p/bin/br_biofetch-rb%type_pkg[ruby] \
--slave %p/bin/br_bioflat br_bioflat
%p/bin/br_bioflat-rb%type_pkg[ruby] \
--slave %p/bin/br_biogetseq br_biogetseq
%p/bin/br_biogetseq-rb%type_pkg[ruby] \
--slave %p/bin/br_pmfetch br_pmfetch
%p/bin/br_pmfetch-rb%type_pkg[ruby]
<<
PreRmScript: <<
if [ $1 != "upgrade" ]; then
update-alternatives --remove bioruby
%p/bin/bioruby-rb%type_pkg[ruby]
fi
<<
DocFiles: COPYING KNOWN_ISSUES.rdoc README.rdoc RELEASE_NOTES.rdoc ChangeLog
doc/*
# Additional Data:
Homepage: http://bioruby.org/
DescPackaging: <<
Former Maintainer: Koen van der Drift <drift...@users.sourceforge.net>
<<
DescDetail: <<
BioRuby project aims to implement integrated environment for Bioinformatics.
Object oriented scripting language Ruby has many good points suitable for
bioinfomatics research. Powerful regular expressions like Perl, purely
object oriented, simple and very clean syntax -- easy to learn for beginners,
easy to use for biologists, powerful enough for developers.
<<
DescPort: <<
Fix "invalid byte sequence in US-ASCII" error in Bio::TestPhyloXML_class_methods
http://wiki.lifesciencedb.jp/mw/index.php/BioRuby
Reported: https://github.com/bioruby/bioruby/issues/84
<<
<<
--- NEW FILE: bioruby-rb.patch ---
--- a/test/unit/bio/db/test_phyloxml.rb
+++ b/test/unit/bio/db/test_phyloxml.rb
@@ -100,6 +100,7 @@ end #end module TestPhyloXMLData
end
def test_new
+ Encoding.default_external="UTF-8"
str = File.read(TestPhyloXMLData.example_xml)
assert_instance_of(Bio::PhyloXML::Parser,
phyloxml = Bio::PhyloXML::Parser.new(str))
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