diff options
Diffstat (limited to 'science/hs-bio')
-rw-r--r-- | science/hs-bio/Makefile | 87 | ||||
-rw-r--r-- | science/hs-bio/distinfo | 3 | ||||
-rw-r--r-- | science/hs-bio/pkg-descr | 6 | ||||
-rw-r--r-- | science/hs-bio/pkg-plist | 61 |
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 |