Add ruby-bio (BioRuby), an integrated environment for Bioinformatics

written in Ruby.

6 files changed, 91 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 852f40bb6dfe..cfe51b3bff48 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -37,6 +37,7 @@
     SUBDIR += py-biopython
     SUBDIR += rasmol
     SUBDIR += recombine
+    SUBDIR += ruby-bio
     SUBDIR += seaview
     SUBDIR += seqio
     SUBDIR += sim4
diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile
new file mode 100644
index 000000000000..b21101ad859f
--- /dev/null
+++ b/biology/ruby-bio/Makefile
@@ -0,0 +1,34 @@
+# New ports collection makefile for:	BioRuby
+# Date created:		24 October 2001
+# Whom:			Akinori MUSHA aka knu <knu@idaemons.org>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	bio
+PORTVERSION=	0.3.20011024
+CATEGORIES=	biology ruby
+MASTER_SITES=	ftp://ftp.bioruby.org/bioruby/src/
+MASTER_SITE_SUBDIR=	knu
+PKGNAMEPREFIX=	${RUBY_PKGNAMEPREFIX}
+DISTNAME=	${PORTNAME}ruby-${PORTVERSION:R}-${PORTVERSION:E}
+EXTRACT_SUFX=	.tgz
+DIST_SUBDIR=	ruby
+
+MAINTAINER=	knu@FreeBSD.org
+
+USE_RUBY=	yes
+USE_RUBY_SETUP=	yes
+RUBY_SETUP=	install.rb
+
+RUBY_SHEBANG_FILES=	${WRKSRC}/bin/dbget
+
+do-install:
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${RUBY_EXAMPLESDIR}/${PORTNAME}
+	${CP} -R ${WRKSRC}/sample/ ${RUBY_EXAMPLESDIR}/${PORTNAME}/
+	${MKDIR} ${RUBY_DOCDIR}/${PORTNAME}
+	${CP} -R ${WRKSRC}/README ${RUBY_DOCDIR}/${PORTNAME}/
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/ruby-bio/distinfo b/biology/ruby-bio/distinfo
new file mode 100644
index 000000000000..dd75c7f93ab2
--- /dev/null
+++ b/biology/ruby-bio/distinfo
@@ -0,0 +1 @@
+MD5 (ruby/bioruby-0.3-20011024.tgz) = b33c40a43ee47236837dad280814384b
diff --git a/biology/ruby-bio/pkg-comment b/biology/ruby-bio/pkg-comment
new file mode 100644
index 000000000000..ea1c5bcb593d
--- /dev/null
+++ b/biology/ruby-bio/pkg-comment
@@ -0,0 +1 @@
+Integrated environment for Bioinformatics written in Ruby
diff --git a/biology/ruby-bio/pkg-descr b/biology/ruby-bio/pkg-descr
new file mode 100644
index 000000000000..c5c49b2421ef
--- /dev/null
+++ b/biology/ruby-bio/pkg-descr
@@ -0,0 +1,4 @@
+BioRuby project aims to implement integrated environment for
+Bioinformatics by using Ruby.
+
+WWW:	http://bioruby.org/index.html.en
diff --git a/biology/ruby-bio/pkg-plist b/biology/ruby-bio/pkg-plist
new file mode 100644
index 000000000000..42fbbfc5b0c7
--- /dev/null
+++ b/biology/ruby-bio/pkg-plist
@@ -0,0 +1,50 @@
+bin/dbget
+%%RUBY_SITELIBDIR%%/bio.rb
+%%RUBY_SITELIBDIR%%/bio/data/aa.rb
+%%RUBY_SITELIBDIR%%/bio/data/codontable.rb
+%%RUBY_SITELIBDIR%%/bio/data/keggorg.rb
+%%RUBY_SITELIBDIR%%/bio/data/na.rb
+%%RUBY_SITELIBDIR%%/bio/db.rb
+%%RUBY_SITELIBDIR%%/bio/db/aaindex.rb
+%%RUBY_SITELIBDIR%%/bio/db/ddbj.rb
+%%RUBY_SITELIBDIR%%/bio/db/genbank.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/brite.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/cell.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/compound.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/enzyme.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/genes.rb
+%%RUBY_SITELIBDIR%%/bio/db/kegg/genome.rb
+%%RUBY_SITELIBDIR%%/bio/db/litdb.rb
+%%RUBY_SITELIBDIR%%/bio/db/medline.rb
+%%RUBY_SITELIBDIR%%/bio/db/prosite.rb
+%%RUBY_SITELIBDIR%%/bio/db/refseq.rb
+%%RUBY_SITELIBDIR%%/bio/db/transfac.rb
+%%RUBY_SITELIBDIR%%/bio/io/dbget.rb
+%%RUBY_SITELIBDIR%%/bio/io/pubmed.rb
+%%RUBY_SITELIBDIR%%/bio/location.rb
+%%RUBY_SITELIBDIR%%/bio/matrix.rb
+%%RUBY_SITELIBDIR%%/bio/pathway.rb
+%%RUBY_SITELIBDIR%%/bio/reference.rb
+%%RUBY_SITELIBDIR%%/bio/sequence.rb
+%%RUBY_SITELIBDIR%%/bio/util/fold.rb
+@dirrm %%RUBY_SITELIBDIR%%/bio/data
+@dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
+@dirrm %%RUBY_SITELIBDIR%%/bio/db
+@dirrm %%RUBY_SITELIBDIR%%/bio/io
+@dirrm %%RUBY_SITELIBDIR%%/bio/util
+@dirrm %%RUBY_SITELIBDIR%%/bio
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fasta2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/fsplit.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2fasta.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gb2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2nuc.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2pep.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genes2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/genome2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/gt2fasta.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/ssearch2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/tfastx2tab.rb
+%%PORTDOCS%%%%RUBY_EXAMPLESDIR%%/bio/vs-genes.rb
+%%PORTDOCS%%@dirrm %%RUBY_EXAMPLESDIR%%/bio
+%%PORTDOCS%%%%RUBY_DOCDIR%%/bio/README
+%%PORTDOCS%%@dirrm %%RUBY_DOCDIR%%/bio