ports/142187: [new port]: haskell port science/hs-bio

Wed Dec 30 22:20:05 UTC 2009

>Number:         142187
>Category:       ports
>Synopsis:       [new port]: haskell port science/hs-bio
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Dec 30 22:20:05 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator:     Jacula Modyun
>Release:        FreeBSD 7.1-PRERELEASE i386
>Organization:
>Environment:
System: FreeBSD splork.wirewater.yow 7.1-PRERELEASE FreeBSD 7.1-PRERELEASE #0: Sat Oct 18 11:22:07 UTC 2008 root at splork.wirewater.yow:/usr/obj/usr/src/sys/JACULA i386

>Description:

bio: A bioinformatics library.

http://blog.malde.org/index.php/the-haskell-bioinformatics-library/

>How-To-Repeat:

>Fix:

--- hs-bio.shar begins here ---
# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	hs-bio
#	hs-bio/Makefile
#	hs-bio/distinfo
#	hs-bio/pkg-plist
#	hs-bio/pkg-descr
#
echo c - hs-bio
mkdir -p hs-bio > /dev/null 2>&1
echo x - hs-bio/Makefile
sed 's/^X//' >hs-bio/Makefile << '8b1308d27c786271a80790f4d5abed5c'
X# New ports collection makefile for: hs-bio
X# Date created:        December 20 2009
X# Whom:                Giuseppe Pilichi aka Jacula Modyun <jacula at gmail.com>
X#
X
XPORTNAME=	bio
XPORTVERSION=	0.4
XCATEGORIES=	science haskell
XMASTER_SITES=	http://hackage.haskell.org/packages/archive/${PORTNAME}/${PORTVERSION}/
XPKGNAMEPREFIX=	hs-
X
XMAINTAINER=	jacula at gmail.com
XCOMMENT=	A bioinformatics library
X
XBUILD_DEPENDS+=	ghc:${PORTSDIR}/lang/ghc \
X		hs-tagsoup>=0.4:${PORTSDIR}/textproc/hs-tagsoup \
X		hs-binary-ghc>=0.5.0.2:${PORTSDIR}/devel/hs-binary-ghc
XRUN_DEPENDS+=	ghc:${PORTSDIR}/lang/ghc \
X		hs-tagsoup>=0.4:${PORTSDIR}/textproc/hs-tagsoup \
X		hs-binary-ghc>=0.5.0.2:${PORTSDIR}/devel/hs-binary-ghc
X
XGHC_VERSION=	6.10.4
XBIO_VERSION=	${PORTVERSION}
X
XGHC_CMD=	${LOCALBASE}/bin/ghc
XSETUP_CMD=	./setup
X
XDATADIR=	${PREFIX}/share/${DISTNAME}
XDOCSDIR=	${PREFIX}/share/doc/${DISTNAME}
XBIO_LIBDIR_REL=	lib/${DISTNAME}
X
XPLIST_SUB=	GHC_VERSION=${GHC_VERSION} \
X		BIO_VERSION=${BIO_VERSION} \
X		BIO_LIBDIR_REL=${BIO_LIBDIR_REL}
X
X.if defined(NOPORTDOCS)
XPLIST_SUB+=	NOPORTDOCS=""
X.else
XPLIST_SUB+=	NOPORTDOCS="@comment "
X.endif
X
X.if !defined(NOPORTDOCS)
X
XPORT_HADDOCK!=	(cd  ${.CURDIR}/../../lang/ghc && ${MAKE} -V PORT_HADDOCK)
X.if !empty(PORT_HADDOCK:M?0)
XBUILD_DEPENDS+=	haddock:${PORTSDIR}/devel/hs-haddock
X.endif
XBUILD_DEPENDS+=	HsColour:${PORTSDIR}/print/hs-hscolour
X
XHSCOLOUR_VERSION=	1.15
XHSCOLOUR_DATADIR=	${PREFIX}/share/hscolour-${HSCOLOUR_VERSION}
X
XPORTDOCS=	*
X.endif
X
X.SILENT:
X
Xdo-configure:
X	cd ${WRKSRC} && ${GHC_CMD} --make Setup.hs -o setup -package Cabal \
X		     && ${SETUP_CMD} configure --haddock-options=-w --prefix=${PREFIX}
X
Xdo-build:
X	cd ${WRKSRC} && ${SETUP_CMD} build \
X		     && ${SETUP_CMD} register --gen-script
X
X.if !defined(NOPORTDOCS)
X	cd ${WRKSRC} && ${SETUP_CMD} haddock --hyperlink-source \
X					     --hscolour-css=${HSCOLOUR_DATADIR}/hscolour.css
X.endif
X
Xdo-install:
X	cd ${WRKSRC} && ${SETUP_CMD} install \
X		     && ${INSTALL_SCRIPT} register.sh ${PREFIX}/${BIO_LIBDIR_REL}/register.sh
X
Xpost-install:
X	${RM} -f ${PREFIX}/lib/ghc-${GHC_VERSION}/package.conf.old
X
X.include <bsd.port.mk>
8b1308d27c786271a80790f4d5abed5c
echo x - hs-bio/distinfo
sed 's/^X//' >hs-bio/distinfo << 'b2941416e0c3d93fa96f8db1a4930bcc'
XMD5 (bio-0.4.tar.gz) = 339b6d5a14a04a4049c99e08892d8d25
XSHA256 (bio-0.4.tar.gz) = fb53411637cab2150880e6ea0319984e5e45ee90275fc2dd629cb86fc4f048d9
XSIZE (bio-0.4.tar.gz) = 79415
b2941416e0c3d93fa96f8db1a4930bcc
echo x - hs-bio/pkg-plist
sed 's/^X//' >hs-bio/pkg-plist << '358d7e778a0563ca7dc36415792a24e6'
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/AAlign.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/ACE.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/AlignData.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Blast.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastData.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastFlat.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/BlastXML.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Bowtie.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Matrices.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Multiple.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/QAlign.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/SAlign.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment/Soap.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Clustering.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/Escape.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/Feature.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/FeatureHier.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/FeatureHierSequences.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3/SGD.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/ContigLocation.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/LocMap.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Location.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/OnSeq.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Position.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/SeqLocMap.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/SeqLocation.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location/Strand.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Entropy.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/FastQ.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Fasta.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/GOA.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/GeneOntology.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/HashWord.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/KEGG.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/Phd.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SFF.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SFF_name.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/SeqData.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence/TwoBit.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util/Parsex.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util/TestBase.hi
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/HSbio-%%BIO_VERSION%%.o
X%%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/libHSbio-%%BIO_VERSION%%.a
X%%BIO_LIBDIR_REL%%/register.sh
X%%DATADIR%%/README
X%%NOPORTDOCS%%%%DOCSDIR%%/LICENSE
X%%NOPORTDOCS%%@dirrmtry %%DOCSDIR%%
X at dirrmtry %%DATADIR%%
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio
X at dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%
X at dirrm %%BIO_LIBDIR_REL%%
X at exec /bin/sh %D/%%BIO_LIBDIR_REL%%/register.sh
X at exec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old
X at unexec %D/bin/ghc-pkg unregister bio
X at unexec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old
358d7e778a0563ca7dc36415792a24e6
echo x - hs-bio/pkg-descr
sed 's/^X//' >hs-bio/pkg-descr << '26a1d196401d90421a7705c6901ef42b'
XThis is a collection of data structures and algorithms useful for
Xbuilding bioinformatics-related tools and utilities.
XCurrent list of features includes: a Sequence data type supporting
Xprotein and nucleotide sequences and conversion between them.
X
XWWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
26a1d196401d90421a7705c6901ef42b
exit
--- hs-bio.shar ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted: