Date: Wed, 30 Dec 2009 14:19:31 -0800 (PST) From: Jacula Modyun <jacula@gmail.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/142187: [new port]: haskell port science/hs-bio Message-ID: <200912302219.nBUMJU8n094028@splork.wirewater.yow> Resent-Message-ID: <200912302220.nBUMK5Il015599@freefall.freebsd.org>
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>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@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@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@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@dirrmtry %%DATADIR%% X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Util X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Sequence X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Location X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/GFF3 X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio/Alignment X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%%/Bio X@dirrm %%BIO_LIBDIR_REL%%/ghc-%%GHC_VERSION%% X@dirrm %%BIO_LIBDIR_REL%% X@exec /bin/sh %D/%%BIO_LIBDIR_REL%%/register.sh X@exec /bin/rm -f %D/lib/ghc-%%GHC_VERSION%%/package.conf.old X@unexec %D/bin/ghc-pkg unregister bio X@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:
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