Index: head/biology/consed/Makefile =================================================================== --- head/biology/consed/Makefile (revision 383308) +++ head/biology/consed/Makefile (revision 383309) @@ -1,83 +1,85 @@ # Created by: Motomichi Matsuzaki # $FreeBSD$ PORTNAME= consed PORTVERSION= 27.0 CATEGORIES= biology # MASTER_SITES= http://www.phrap.org/consed/distributions/${PORTVERSION}/ MASTER_SITES= http://bozeman.mbt.washington.edu/consed/distributions/${PORTVERSION}/ DISTNAME= ${PORTNAME}_linux MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Graphical tool for editing Phrap assemblies +BROKEN= Unfetchable + RUN_DEPENDS= phred:${PORTSDIR}/biology/phred \ phrap:${PORTSDIR}/biology/phrap CONFLICTS_INSTALL= phd2fasta-[0-9]* SUB_FILES= pkg-message USES= perl5 shebangfix USE_LINUX= yes USE_LINUX_APPS= xorglibs ONLY_FOR_ARCHS= i386 amd64 MYSHEBANG= bin/ace2Fasta.perl \ bin/tagRepeats.perl \ bin/selectRegions.perl \ bin/selectOneRegion.perl \ bin/revertToUneditedRead \ bin/removeReads \ bin/phredPhrap.orig \ bin/phredPhrap \ bin/phd2Ace.perl \ bin/orderPrimerPairs.perl \ bin/makeRegionsFile.perl \ bin/makePhdBall.perl \ bin/lib2Phd.perl \ bin/fixContigEnd.perl \ bin/findSequenceMatchesForConsed.perl \ bin/revert_fof \ bin/filter454Reads.perl \ bin/fastq2Phrap.perl \ bin/fasta2PhdBall.perl \ bin/fasta2Phd.perl \ bin/fasta2Ace.perl \ bin/determineReadTypes.perl \ bin/countEditedBases.perl \ bin/bam2Ace.perl \ bin/amplifyTranscripts.perl \ bin/alignSolexaReads2Refs.perl \ bin/alignRNA2Genomic.perl \ bin/addSolexaReads.perl \ bin/addSangerReads.perl \ bin/addReads2Consed.perl \ bin/add454Reads.perl \ bin/ace2Oligos.perl \ bin/transferConsensusTags.perl \ bin/ace2fof \ bin/ace2OligosWithComments.perl \ bin/sff2phd.perl \ bin/recover_consensus_tags \ bin/phredPhrapWithPhdBalls \ bin/cons.perl \ bin/acestatus.pl \ bin/aceContigs2Phds.perl \ bin/sff2phd_Samborskyy RESTRICTED= Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use. .if defined(PACKAGE_BUILDING) IGNORE= distribution files must be obtained via the authors .endif NO_WRKSUBDIR= yes NO_BUILD= yes do-install: ${MKDIR} ${STAGEDIR}${DATADIR} ${LN} -sf ../../bin ${STAGEDIR}${DATADIR}/bin (cd ${WRKSRC}; ${ENV} CC=${CC} ./installConsed.perl consed_linux32bit ${STAGEDIR}${DATADIR}) ${LN} -sf ../../../etc/PhredPar/phredpar.dat ${STAGEDIR}${DATADIR}/lib/phredpar.dat cd ${STAGEDIR}${PREFIX} && ${ECHO_CMD} ${MYSHEBANG} | ${XARGS} ${SED} -i '' ${_SHEBANG_REINPLACE_ARGS} .include Index: head/biology/migrate/Makefile =================================================================== --- head/biology/migrate/Makefile (revision 383308) +++ head/biology/migrate/Makefile (revision 383309) @@ -1,62 +1,64 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= migrate PORTVERSION= 3.6.7 CATEGORIES= biology MASTER_SITES= http://popgen.sc.fsu.edu/currentversions/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= ports@FreeBSD.org COMMENT= Program to estimate population sizes and migration rates +BROKEN= unfetchable + GNU_CONFIGURE= yes CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}" MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu \ -DPRETTY -lstdc++" WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src PLIST_SUB+= PORTNAME=${PORTNAME} PORTDOCS= HISTORY README README_PARALLEL_GENERAL ${PORTNAME}.html PORTEXAMPLES= * EXTRACT_AFTER_ARGS=--exclude zlib # XXX should be converted to OptionsNG .if defined(WITH_THREAD_PRETTY) ALL_TARGET= thread-pretty .elif defined(WITH_PRETTY) ALL_TARGET= pretty .elif defined(WITH_THREAD) ALL_TARGET= thread .else ALL_TARGET= all .endif OPTIONS_DEFINE= DOCS EXAMPLES .include post-patch: @${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${STAGEDIR}${PREFIX}/bin ${LN} -sf ${PORTNAME}-n ${STAGEDIR}${PREFIX}/bin/${PORTNAME} ${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 \ ${STAGEDIR}${MAN1PREFIX}/man/man1 ${LN} -sf ${PORTNAME}.1 \ ${STAGEDIR}${MAN1PREFIX}/man/man1/${PORTNAME}-n.1 @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PORTDOCS:S,^,${WRKSRC}/../,} ${STAGEDIR}${DOCSDIR} @${MKDIR} ${STAGEDIR}${DOCSDIR}/graphics ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${STAGEDIR}${DOCSDIR}/graphics @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* \ ${STAGEDIR}${EXAMPLESDIR} .include Index: head/biology/ncbi-blast+/Makefile =================================================================== --- head/biology/ncbi-blast+/Makefile (revision 383308) +++ head/biology/ncbi-blast+/Makefile (revision 383309) @@ -1,58 +1,60 @@ # Created by: Jason Bacon # $FreeBSD$ PORTNAME= blast+ PORTVERSION= 2.2.30 PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ PKGNAMEPREFIX= ncbi- DISTNAME= ncbi-blast-${PORTVERSION}+-src MAINTAINER= jwbacon@tds.net COMMENT= NCBI implementation of Basic Local Alignment Search Tool +BROKEN= Unfetchable + LICENSE= Public_domain LICENSE_NAME= Public Domain LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept LIB_DEPENDS= libpcre.so:${PORTSDIR}/devel/pcre \ libbz2.so:${PORTSDIR}/archivers/bzip2 RUN_DEPENDS= p5-List-MoreUtils>=0:${PORTSDIR}/lang/p5-List-MoreUtils WRKSRC= ${WRKDIR}/${DISTNAME}/c++ GNU_CONFIGURE= yes USES= gmake shebangfix perl5 python SHEBANG_FILES= src/app/blast/legacy_blast.pl \ src/app/blast/update_blastdb.pl \ src/app/winmasker/windowmasker_2.2.22_adapter.py # Requires openmp USE_GCC= yes USE_LDCONFIG= yes # The test for amq can hang, but amq is not needed so just avoid the test CONFIGURE_ENV= ncbi_cv_prog_amq_w=no # configure chooses /usr/local/bin/ar with no flags # FreeBSD boost port flagged by configure as untested version CONFIGURE_ARGS+=AR="ar cr" --without-boost # Fix "undefined _ThreadRuneLocale" error on 10.0 # Fix unknown options in configure # Add staging support to configure-generated Makefile post-patch: ${REINPLACE_CMD} \ -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' \ -e '/--infodir=DIR/d' \ -e '/--mandir=DIR/d' \ ${WRKSRC}/src/build-system/configure ${REINPLACE_CMD} -e 's|@prefix@|${STAGEDIR}@prefix@|g' \ ${WRKSRC}/src/build-system/Makefile.in.top post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so .include Index: head/biology/njplot/Makefile =================================================================== --- head/biology/njplot/Makefile (revision 383308) +++ head/biology/njplot/Makefile (revision 383309) @@ -1,51 +1,53 @@ # Created by: Motomichi Matsuzaki # $FreeBSD$ PORTNAME= njplot PORTVERSION= 2.1 PORTREVISION= 3 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/ MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Phylogenetic tree drawing program capable of interactive manipulation +BROKEN= Unfetchable + OPTIONS_DEFINE= DOCS X11 OPTIONS_DEFAULT= DOCS X11 .include .if ${PORT_OPTIONS:MX11} BUILD_DEPENDS= ${LOCALBASE}/lib/ncbi/libvibrant.a:${PORTSDIR}/biology/ncbi-toolkit USE_XORG= x11 xt xmu xp USES= motif .endif MAKEFILE= makefile BINARIES= newicktops newicktotxt .if ${PORT_OPTIONS:MX11} BINARIES+= njplot unrooted .endif .for file in ${BINARIES} PLIST_FILES+= bin/${file} .endfor PORTDOCS= njplot.help njplot.html njplot.gif MAN_1= njplot.1 unrooted.1 PLIST_FILES+= man/man1/njplot.1.gz \ man/man1/unrooted.1.gz .if !${PORT_OPTIONS:MX11} post-patch: ${REINPLACE_CMD} -e 's|njplot.*unrooted||' ${WRKSRC}/makefile .endif do-install: ${INSTALL_PROGRAM} ${BINARIES:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${MAN_1:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/man/man1 ${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_MAN} ${PORTDOCS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} .include Index: head/biology/ortep3/Makefile =================================================================== --- head/biology/ortep3/Makefile (revision 383308) +++ head/biology/ortep3/Makefile (revision 383309) @@ -1,57 +1,59 @@ # Created by: Ryo MIYAMOTO # $FreeBSD$ PORTNAME= ortep3 PORTVERSION= 1.0.3 PORTREVISION= 9 CATEGORIES= biology MASTER_SITES= http://www.ccl.net/cca/software/SOURCES/FORTRAN/ortep/:Z \ ftp://ftp.ornl.gov/pub/ortep/src/:f DISTFILES= ortep.tar.Z:Z ortep.f:f EXTRACT_ONLY= ortep.tar.Z MAINTAINER= ports@FreeBSD.org COMMENT= Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure +BROKEN= Unfetchable + PGPLOT_LIB_DEPENDS= libpgplot.so:${PORTSDIR}/graphics/pgplot USES= fortran WRKSRC= ${WRKDIR}/ortep/src MAKE_ARGS= LFLAGS="${LDFLAGS}" PGPLOT_LDFLAGS= -L${LOCALBASE}/lib -lpgplot -lX11 PLIST_FILES+= bin/ortep3 PORTDOCS= * PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES PGPLOT PGPLOT_DESC= Fortran subroutine package for drawing graphs .include .if ${PORT_OPTIONS:MPGPLOT} EXTRA_PATCHES= ${FILESDIR}/extra-patch-aa .endif post-extract: ${MV} ${WRKSRC}/ortep.f ${WRKSRC}/ortep.f-1.0 ${CP} ${DISTDIR}/ortep.f ${WRKSRC}/ortep.f pre-build: ${CP} ${FILESDIR}/Makefile.ortep3 ${WRKSRC}/Makefile do-install: ${INSTALL_PROGRAM} ${WRKSRC}/ortep3 ${STAGEDIR}${PREFIX}/bin .if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${STAGEDIR}${DOCSDIR}/src ${INSTALL_DATA} ${WRKSRC}/../README.1st ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/../man/* ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/000readme.txt ${STAGEDIR}${DOCSDIR}/src .endif .if ${PORT_OPTIONS:MEXAMPLES} ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/../examples/* ${STAGEDIR}${EXAMPLESDIR} .endif .include Index: head/biology/p5-Bio-ASN1-EntrezGene/Makefile =================================================================== --- head/biology/p5-Bio-ASN1-EntrezGene/Makefile (revision 383308) +++ head/biology/p5-Bio-ASN1-EntrezGene/Makefile (revision 383309) @@ -1,19 +1,21 @@ # Created by: Mauricio Herrera Cuadra # $FreeBSD$ PORTNAME= Bio-ASN1-EntrezGene PORTVERSION= 1.091 PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= mauricio@arareko.net COMMENT= Regular expression-based Perl Parser for NCBI Entrez Gene +BROKEN= Unfetchable + WRKSRC= ${WRKDIR}/Bio-ASN1-EntrezGene-1.09 USES= perl5 tar:tgz USE_PERL5= configure .include Index: head/biology/paml/Makefile =================================================================== --- head/biology/paml/Makefile (revision 383308) +++ head/biology/paml/Makefile (revision 383309) @@ -1,31 +1,33 @@ # Created by: dbader@eece.unm.edu # $FreeBSD$ PORTNAME= paml PORTVERSION= 4.8 CATEGORIES= biology MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/ DISTNAME= ${PORTNAME}${PORTVERSION} MAINTAINER= jrm@ftfl.ca COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML) +BROKEN= Unfetchable + USES= gmake tar:tgz WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION}/src MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS}" BINARIES= baseml basemlg chi2 codeml evolver pamp yn00 DOC_FILES= pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt OPTIONS_DEFINE= DOCS do-install: .for f in ${BINARIES} ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin .endfor @${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${DOC_FILES} ${INSTALL_DATA} ${WRKDIR}/${PORTNAME}${PORTVERSION}/doc/${f} ${STAGEDIR}${DOCSDIR} .endfor .include Index: head/biology/platon/Makefile =================================================================== --- head/biology/platon/Makefile (revision 383308) +++ head/biology/platon/Makefile (revision 383309) @@ -1,51 +1,52 @@ # Created by: Ryo MIYAMOTO # $FreeBSD$ PORTNAME= platon PORTVERSION= 2015.03.05 CATEGORIES= biology MASTER_SITES= http://www.cryst.chem.uu.nl/spek/xraysoft/unix/ \ http://www.platonsoft.nl/spek/xraysoft/ DISTNAME= platon MAINTAINER= ports@FreeBSD.org COMMENT= Tool for viewing molecular/crystallographic structures # PLATON may be used free of charge by the academic community under # the condition that it is not redistributed for a current & fresh copy. # There is a charge of US$ 5000 for commercial users. NO_CDROM= free for academic, US$ 5000 for commercial users +BROKEN= Unfetchable USES= fortran USE_XORG= x11 SAMPLES= azt.dat bucky.spf c476.spf c540.cart3d check.def cubane.spf \ cyto.spf ml.pdb s810c.cif s913a.res sucrose.spf TESTDATADIR= ABSORB_EXAMPLE ABSTOMPA_EXAMPLE ABSTOMPA_TEST ADDSYM_EXAMPLE \ ASYM_EXAMPLE MULABS_EXAMPLE PSICOR_EXAMPLE SQUEEZE_EXAMPLE OPTIONS_DEFINE= DOCS MAKEFILE= ${FILESDIR}/Makefile .include pre-patch: ${GUNZIP_CMD} ${WRKSRC}/platon.f.gz ${WRKSRC}/xdrvr.c.gz do-install: ${INSTALL_PROGRAM} ${WRKDIR}/${DISTNAME}/platon \ ${STAGEDIR}${PREFIX}/bin ${LN} -fs platon ${STAGEDIR}${PREFIX}/bin/pluton .if ${PORT_OPTIONS:MDOCS} ${MKDIR} ${STAGEDIR}${DOCSDIR} ${MV} ${WRKDIR}/${DISTNAME}/README* ${STAGEDIR}${DOCSDIR}/ ${MV} ${SAMPLES:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}/ ${MV} ${WRKSRC}/platon_html.tar.gz \ ${STAGEDIR}${DOCSDIR} ${MV} ${WRKSRC}/TEST ${STAGEDIR}${DOCSDIR}/ ${FIND} ${STAGEDIR}${DOCSDIR} -type f -print0 | \ ${XARGS} -0 ${CHMOD} ${_SHAREMODE} .endif .include Index: head/biology/povchem/Makefile =================================================================== --- head/biology/povchem/Makefile (revision 383308) +++ head/biology/povchem/Makefile (revision 383309) @@ -1,46 +1,47 @@ # Created by: frankch@waru.life.nthu.edu.tw # $FreeBSD$ PORTNAME= povchem PORTVERSION= 1.0 PORTREVISION= 7 CATEGORIES= biology graphics MASTER_SITES= http://www.chemicalgraphics.com/paul/PC_Dist/v1.00/ DISTFILES= povchem.c \ povchem.cfg \ periodic.tab DIST_SUBDIR= povchem EXTRACT_ONLY= # MAINTAINER= ports@FreeBSD.org COMMENT= Simple yet powerful tool to generate POV from a PDB file RUN_DEPENDS= povray:${PORTSDIR}/graphics/povray-meta +BROKEN= Unfetchable NO_WRKSUBDIR= yes USES= dos2unix CPPFLAGS+= -DDATADIR=\"${DATADIR}\" \ -DSYSCONFDIR=\"${PREFIX}/etc\" PLIST_FILES= bin/povchem etc/povchem.cfg %%DATADIR%%/periodic.tab post-extract: @(cd ${DISTDIR}/${DIST_SUBDIR} && ${TAR} -cf - ${DISTFILES}) | \ (cd ${WRKSRC} && ${TAR} -xf -) post-patch: @${REINPLACE_CMD} -e \ 's|%%LOCALBASE%%|${LOCALBASE}|' ${WRKSRC}/povchem.cfg do-build: cd ${WRKSRC} && ${CC} ${CFLAGS} ${CPPFLAGS} -o povchem povchem.c -lm do-install: ${INSTALL_PROGRAM} ${WRKSRC}/povchem ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${WRKSRC}/povchem.cfg ${STAGEDIR}${PREFIX}/etc @${MKDIR} ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/periodic.tab ${STAGEDIR}${DATADIR} .include Index: head/biology/seaview/Makefile =================================================================== --- head/biology/seaview/Makefile (revision 383308) +++ head/biology/seaview/Makefile (revision 383309) @@ -1,54 +1,56 @@ # Created by: frankch@waru.life.nthu.edu.tw # $FreeBSD$ PORTNAME= seaview PORTVERSION= 4.5.4 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= http://doua.prabi.fr/software/seaview_data/ \ ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= bofh@FreeBSD.org COMMENT= Multiple DNA/protein sequence alignment editor LICENSE= GPLv3 +BROKEN= Unfetchable + LIB_DEPENDS= libfltk.so:${PORTSDIR}/x11-toolkits/fltk \ libpng.so:${PORTSDIR}/graphics/png WRKSRC= ${WRKDIR}/${PORTNAME} USES= gmake USE_XORG= xext xft xinerama MAKE_ENV= HELPFILE='-DDEFAULT_HELPFILE=\"${DATADIR}/seaview.html\"' \ PHYMLNAME='-DPHYMLNAME=\"phyml\"' \ IFLTK='-I${LOCALBASE}/include' \ LFLTK='-L${LOCALBASE}/lib' \ USE_XFT='-DUSE_XFT' \ OPT="${CFLAGS}" ALL_TARGET= ${PORTNAME} PLIST_FILES= bin/seaview man/man1/seaview.1.gz %%DATADIR%%/seaview.html \ share/pixmaps/seaview.xpm DESKTOP_ENTRIES="SeaView" "" "${PREFIX}/share/pixmaps/seaview.xpm" "seaview" \ "Biology;Science;" true post-patch: ${REINPLACE_CMD} -e \ 's|^\(CC\) |#\1 | ; \ s|^\(CXX\) |#\1 |' ${WRKSRC}/Makefile do-install: (cd ${WRKSRC} && ${INSTALL_PROGRAM} seaview \ ${STAGEDIR}${PREFIX}/bin) (cd ${WRKSRC} && ${INSTALL_MAN} seaview.1 \ ${STAGEDIR}${MANPREFIX}/man/man1) ${MKDIR} ${STAGEDIR}${DATADIR} (cd ${WRKSRC} && ${INSTALL_DATA} seaview.html \ ${STAGEDIR}${DATADIR}) (cd ${WRKSRC} && ${INSTALL_DATA} seaview.xpm \ ${STAGEDIR}${PREFIX}/share/pixmaps) .include