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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/ PR: ports/142187 Submitted by: Jacula Modyun <jacula(at)gmail.com>
This commit is contained in:
parent
81793cc1be
commit
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Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=247041
@ -63,6 +63,7 @@
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SUBDIR += hdf
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SUBDIR += hdf5
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SUBDIR += hdf5-18
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SUBDIR += hs-bio
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SUBDIR += ics
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SUBDIR += isaac-cfd
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SUBDIR += jmol
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87
science/hs-bio/Makefile
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87
science/hs-bio/Makefile
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# New ports collection makefile for: hs-bio
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# Date created: December 20 2009
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# Whom: Giuseppe Pilichi aka Jacula Modyun <jacula@gmail.com>
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#
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# $FreeBSD$
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#
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PORTNAME= bio
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PORTVERSION= 0.4
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CATEGORIES= science haskell
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MASTER_SITES= http://hackage.haskell.org/packages/archive/${PORTNAME}/${PORTVERSION}/
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PKGNAMEPREFIX= hs-
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MAINTAINER= jacula@gmail.com
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COMMENT= A Haskell bioinformatics library
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BUILD_DEPENDS+= ghc:${PORTSDIR}/lang/ghc \
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hs-tagsoup>=0.4:${PORTSDIR}/textproc/hs-tagsoup \
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hs-binary-ghc>=0.5.0.2:${PORTSDIR}/devel/hs-binary-ghc
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RUN_DEPENDS+= ghc:${PORTSDIR}/lang/ghc \
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hs-tagsoup>=0.4:${PORTSDIR}/textproc/hs-tagsoup \
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hs-binary-ghc>=0.5.0.2:${PORTSDIR}/devel/hs-binary-ghc
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GHC_VERSION= 6.10.4
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BIO_VERSION= ${PORTVERSION}
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GHC_CMD= ${LOCALBASE}/bin/ghc
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SETUP_CMD= ./setup
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DATADIR= ${PREFIX}/share/${DISTNAME}
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PORTDATA= *
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DOCSDIR= ${PREFIX}/share/doc/${DISTNAME}
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BIO_LIBDIR_REL= lib/${DISTNAME}
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PLIST_SUB= GHC_VERSION=${GHC_VERSION} \
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BIO_VERSION=${BIO_VERSION} \
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BIO_LIBDIR_REL=${BIO_LIBDIR_REL}
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.if defined(NOPORTDOCS)
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PLIST_SUB+= NOPORTDOCS=""
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.else
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PLIST_SUB+= NOPORTDOCS="@comment "
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.endif
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.if !defined(NOPORTDOCS)
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PORT_HADDOCK!= (cd ${.CURDIR}/../../lang/ghc && ${MAKE} -V PORT_HADDOCK)
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.if !empty(PORT_HADDOCK:M?0)
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BUILD_DEPENDS+= haddock:${PORTSDIR}/devel/hs-haddock
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.endif
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BUILD_DEPENDS+= HsColour:${PORTSDIR}/print/hs-hscolour
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HSCOLOUR_VERSION= 1.15
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HSCOLOUR_DATADIR= ${PREFIX}/share/hscolour-${HSCOLOUR_VERSION}
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PORTDOCS= *
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.endif
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.SILENT:
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do-configure:
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cd ${WRKSRC} && ${GHC_CMD} --make Setup.hs -o setup -package Cabal
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.if !defined(NOPORTDATA)
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cd ${WRKSRC} && ${SETUP_CMD} configure --haddock-options=-w --prefix=${PREFIX}
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.else
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cd ${WRKSRC} && ${SETUP_CMD} configure --haddock-options=-w --prefix=${PREFIX} \
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--datadir='' --datasubdir='' --docdir='${DOCSDIR}'
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.endif
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do-build:
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cd ${WRKSRC} && ${SETUP_CMD} build \
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&& ${SETUP_CMD} register --gen-script
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.if !defined(NOPORTDOCS)
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cd ${WRKSRC} && ${SETUP_CMD} haddock --hyperlink-source \
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--hscolour-css=${HSCOLOUR_DATADIR}/hscolour.css
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.endif
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do-install:
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cd ${WRKSRC} && ${SETUP_CMD} install \
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&& ${INSTALL_SCRIPT} register.sh ${PREFIX}/${BIO_LIBDIR_REL}/register.sh
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post-install:
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${RM} -f ${PREFIX}/lib/ghc-${GHC_VERSION}/package.conf.old
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.include <bsd.port.mk>
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3
science/hs-bio/distinfo
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3
science/hs-bio/distinfo
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MD5 (bio-0.4.tar.gz) = 339b6d5a14a04a4049c99e08892d8d25
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SHA256 (bio-0.4.tar.gz) = fb53411637cab2150880e6ea0319984e5e45ee90275fc2dd629cb86fc4f048d9
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SIZE (bio-0.4.tar.gz) = 79415
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6
science/hs-bio/pkg-descr
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6
science/hs-bio/pkg-descr
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This is a collection of Haskell data structures and algorithms useful for
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building bioinformatics-related tools and utilities.
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Current list of features includes: a Sequence data type supporting
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protein and nucleotide sequences and conversion between them.
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WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
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science/hs-bio/pkg-plist
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61
science/hs-bio/pkg-plist
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@comment $FreeBSD$
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/AAlign.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/ACE.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/AlignData.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Blast.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastData.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastFlat.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastXML.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Bowtie.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Matrices.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Multiple.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/QAlign.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/SAlign.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Soap.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Clustering.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/Escape.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/Feature.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/FeatureHier.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/FeatureHierSequences.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/SGD.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/ContigLocation.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/LocMap.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Location.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/OnSeq.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Position.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/SeqLocMap.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/SeqLocation.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Strand.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Entropy.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/FastQ.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Fasta.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/GOA.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/GeneOntology.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/HashWord.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/KEGG.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Phd.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SFF.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SFF_name.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SeqData.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/TwoBit.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util/Parsex.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util/TestBase.hi
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/HSbio-%%BIO_VERSION%%.o
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%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/libHSbio-%%BIO_VERSION%%.a
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%%BIO_LIBDIR_REL%%/register.sh
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%%NOPORTDOCS%%%%DOCSDIR%%/LICENSE
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%%NOPORTDOCS%%@dirrmtry %%DOCSDIR%%
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio
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@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%
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@dirrm %%BIO_LIBDIR_REL%%
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@exec /bin/sh %D/%%BIO_LIBDIR_REL%%/register.sh
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@exec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old
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@unexec %D/bin/ghc-pkg unregister bio
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@unexec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old
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