4 files changed, 157 insertions, 0 deletions

diff --git a/science/hs-bio/Makefile b/science/hs-bio/Makefile
new file mode 100644
index 000000000000..5544cfabd58f
--- /dev/null
+++ b/science/hs-bio/Makefile
@@ -0,0 +1,87 @@
+# New ports collection makefile for: hs-bio
+# Date created:        December 20 2009
+# Whom:                Giuseppe Pilichi aka Jacula Modyun <jacula@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	bio
+PORTVERSION=	0.4
+CATEGORIES=	science haskell
+MASTER_SITES=	http://hackage.haskell.org/packages/archive/${PORTNAME}/${PORTVERSION}/
+PKGNAMEPREFIX=	hs-
+
+MAINTAINER=	jacula@gmail.com
+COMMENT=	A Haskell bioinformatics library
+
+BUILD_DEPENDS+=	ghc:${PORTSDIR}/lang/ghc \
+		hs-tagsoup>=0.4:${PORTSDIR}/textproc/hs-tagsoup \
+		hs-binary-ghc>=0.5.0.2:${PORTSDIR}/devel/hs-binary-ghc
+RUN_DEPENDS+=	ghc:${PORTSDIR}/lang/ghc \
+		hs-tagsoup>=0.4:${PORTSDIR}/textproc/hs-tagsoup \
+		hs-binary-ghc>=0.5.0.2:${PORTSDIR}/devel/hs-binary-ghc
+
+GHC_VERSION=	6.10.4
+BIO_VERSION=	${PORTVERSION}
+
+GHC_CMD=	${LOCALBASE}/bin/ghc
+SETUP_CMD=	./setup
+
+DATADIR=	${PREFIX}/share/${DISTNAME}
+PORTDATA=	*
+
+DOCSDIR=	${PREFIX}/share/doc/${DISTNAME}
+BIO_LIBDIR_REL=	lib/${DISTNAME}
+
+PLIST_SUB=	GHC_VERSION=${GHC_VERSION} \
+		BIO_VERSION=${BIO_VERSION} \
+		BIO_LIBDIR_REL=${BIO_LIBDIR_REL}
+
+.if defined(NOPORTDOCS)
+PLIST_SUB+=	NOPORTDOCS=""
+.else
+PLIST_SUB+=	NOPORTDOCS="@comment "
+.endif
+
+.if !defined(NOPORTDOCS)
+
+PORT_HADDOCK!=	(cd  ${.CURDIR}/../../lang/ghc && ${MAKE} -V PORT_HADDOCK)
+.if !empty(PORT_HADDOCK:M?0)
+BUILD_DEPENDS+=	haddock:${PORTSDIR}/devel/hs-haddock
+.endif
+BUILD_DEPENDS+=	HsColour:${PORTSDIR}/print/hs-hscolour
+
+HSCOLOUR_VERSION=	1.15
+HSCOLOUR_DATADIR=	${PREFIX}/share/hscolour-${HSCOLOUR_VERSION}
+
+PORTDOCS=	*
+.endif
+
+.SILENT:
+
+do-configure:
+	cd ${WRKSRC} && ${GHC_CMD} --make Setup.hs -o setup -package Cabal
+.if !defined(NOPORTDATA)
+	cd ${WRKSRC} && ${SETUP_CMD} configure --haddock-options=-w --prefix=${PREFIX}
+.else
+	cd ${WRKSRC} && ${SETUP_CMD} configure --haddock-options=-w --prefix=${PREFIX} \
+	    --datadir='' --datasubdir='' --docdir='${DOCSDIR}'
+.endif
+
+do-build:
+	cd ${WRKSRC} && ${SETUP_CMD} build \
+		     && ${SETUP_CMD} register --gen-script
+
+.if !defined(NOPORTDOCS)
+	cd ${WRKSRC} && ${SETUP_CMD} haddock --hyperlink-source \
+					     --hscolour-css=${HSCOLOUR_DATADIR}/hscolour.css
+.endif
+
+do-install:
+	cd ${WRKSRC} && ${SETUP_CMD} install \
+		     && ${INSTALL_SCRIPT} register.sh ${PREFIX}/${BIO_LIBDIR_REL}/register.sh
+
+post-install:
+	${RM} -f ${PREFIX}/lib/ghc-${GHC_VERSION}/package.conf.old
+
+.include <bsd.port.mk>
diff --git a/science/hs-bio/distinfo b/science/hs-bio/distinfo
new file mode 100644
index 000000000000..3239c462b91d
--- /dev/null
+++ b/science/hs-bio/distinfo
@@ -0,0 +1,3 @@
+MD5 (bio-0.4.tar.gz) = 339b6d5a14a04a4049c99e08892d8d25
+SHA256 (bio-0.4.tar.gz) = fb53411637cab2150880e6ea0319984e5e45ee90275fc2dd629cb86fc4f048d9
+SIZE (bio-0.4.tar.gz) = 79415
diff --git a/science/hs-bio/pkg-descr b/science/hs-bio/pkg-descr
new file mode 100644
index 000000000000..4d255476072e
--- /dev/null
+++ b/science/hs-bio/pkg-descr
@@ -0,0 +1,6 @@
+This is a collection of Haskell data structures and algorithms useful for
+building bioinformatics-related tools and utilities.
+Current list of features includes: a Sequence data type supporting
+protein and nucleotide sequences and conversion between them.
+
+WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
diff --git a/science/hs-bio/pkg-plist b/science/hs-bio/pkg-plist
new file mode 100644
index 000000000000..135a5026dde4
--- /dev/null
+++ b/science/hs-bio/pkg-plist
@@ -0,0 +1,61 @@
+@comment $FreeBSD$
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/AAlign.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/ACE.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/AlignData.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Blast.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastData.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastFlat.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastXML.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Bowtie.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Matrices.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Multiple.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/QAlign.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/SAlign.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Soap.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Clustering.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/Escape.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/Feature.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/FeatureHier.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/FeatureHierSequences.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/SGD.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/ContigLocation.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/LocMap.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Location.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/OnSeq.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Position.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/SeqLocMap.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/SeqLocation.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Strand.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Entropy.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/FastQ.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Fasta.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/GOA.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/GeneOntology.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/HashWord.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/KEGG.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Phd.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SFF.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SFF_name.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SeqData.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/TwoBit.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util/Parsex.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util/TestBase.hi
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/HSbio-%%BIO_VERSION%%.o
+%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/libHSbio-%%BIO_VERSION%%.a
+%%BIO_LIBDIR_REL%%/register.sh
+%%NOPORTDOCS%%%%DOCSDIR%%/LICENSE
+%%NOPORTDOCS%%@dirrmtry %%DOCSDIR%%
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio
+@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%
+@dirrm %%BIO_LIBDIR_REL%%
+@exec /bin/sh %D/%%BIO_LIBDIR_REL%%/register.sh
+@exec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old
+@unexec %D/bin/ghc-pkg unregister bio
+@unexec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old