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This is a collection of Haskell data structures and algorithms useful for

Browse Source 
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:
Gabor Pali 2010-01-03 05:02:13 +00:00
parent 81793cc1be
commit 80bc5be124
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=247041
5 changed files with 158 additions and 0 deletions
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1
science/Makefile
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@ -63,6 +63,7 @@
SUBDIR += hdf
SUBDIR += hdf5
SUBDIR += hdf5-18
SUBDIR += hs-bio
SUBDIR += ics
SUBDIR += isaac-cfd
SUBDIR += jmol

87
science/hs-bio/Makefile Normal file
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@ -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>

3
science/hs-bio/distinfo Normal file
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@ -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

6
science/hs-bio/pkg-descr Normal file
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@ -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/

61
science/hs-bio/pkg-plist Normal file
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@ -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