Index: head/biology/ariadne/Makefile =================================================================== --- head/biology/ariadne/Makefile (revision 451981) +++ head/biology/ariadne/Makefile (revision 451982) @@ -1,34 +1,36 @@ # Created by: Fernan Aguero # $FreeBSD$ PORTNAME= ariadne PORTVERSION= 1.3 CATEGORIES= biology MASTER_SITES= http://www.well.ox.ac.uk/ariadne/ MAINTAINER= ports@FreeBSD.org COMMENT= Programs to compare protein sequences and profiles WRKSRC= ${WRKDIR}/SRC-${PORTVERSION} +BROKEN= No public distfiles + PLIST_FILES+= bin/ariadne bin/prospero USES= gmake tar:Z PORTDOCS= README MAKE_ARGS+= CC="${CC}" OPTIONS_DEFINE= DOCS MAKE_JOBS_UNSAFE= yes post-patch: @${REINPLACE_CMD} -e 's|CFLAGS =|CFLAGS +=| ; \ s|-c $$(OPTIMISE)|-c ${CFLAGS} ${OPTIMIZE}|g' \ ${WRKSRC}/Makefile do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/ariadne ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/${OPSYS}/prospero ${STAGEDIR}${PREFIX}/bin @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/README ${STAGEDIR}${DOCSDIR} .include Index: head/biology/biococoa/Makefile =================================================================== --- head/biology/biococoa/Makefile (revision 451981) +++ head/biology/biococoa/Makefile (revision 451982) @@ -1,21 +1,21 @@ # $FreeBSD$ PORTNAME= biococoa PORTVERSION= 2.2.2 PORTREVISION= 3 CATEGORIES= biology gnustep -MASTER_SITES= http://bioinformatics.org/biococoa/downloads/ DEBIAN/pool/main/b/biococoa.app +MASTER_SITES= http://bioinformatics.org/biococoa/downloads/ DISTNAME= biococoa-${PORTVERSION}-src EXTRACT_SUFX= .tgz MAINTAINER= theraven@FreeBSD.org COMMENT= Bioinformatics framework LICENSE= LGPL21 USES= gnustep USE_GNUSTEP= back build WRKSRC= ${WRKDIR}/biococoa-${PORTVERSION} .include Index: head/biology/crux/Makefile =================================================================== --- head/biology/crux/Makefile (revision 451981) +++ head/biology/crux/Makefile (revision 451982) @@ -1,52 +1,53 @@ # Created by: Jason Evans # $FreeBSD$ PORTNAME= crux PORTVERSION= 1.2.0 PORTREVISION= 8 CATEGORIES= biology python MASTER_SITES= http://www.canonware.com/download/Crux/ MAINTAINER= ports@FreeBSD.org COMMENT= Software toolkit for phylogenetic inference LICENSE= BSD2CLAUSE BSD3CLAUSE LICENSE_COMB= multi +BROKEN= No public distfiles BROKEN_aarch64= Fails to link: ImportError: /lib/libgcc_s.so.1: version GCC_4.5.0 required by /usr/local/lib/gcc5/libgfortran.so.3 not found BROKEN_armv6= Fails to link: ImportError: /usr/local/lib/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod" USES= fortran gmake python tar:bzip2 USE_CSTD= gnu99 GNU_CONFIGURE= yes CONFIGURE_ARGS= --datadir=${PREFIX}/lib \ --with-python=${PYTHON_CMD} \ --disable-mpi CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib MAKE_JOBS_UNSAFE= yes OPTIONS_DEFINE= SYS_LINALG SYS_LINALG_DESC= Enable system ATLAS/LAPACK SYS_LINALG_LIB_DEPENDS= libatlas.so:math/atlas SYS_LINALG_CONFIGURE_ENABLE= sys-linalg post-patch: @${REINPLACE_CMD} -e '/altivec/s|-f|-m|' ${WRKSRC}/configure @${REINPLACE_CMD} -e \ 's|\([[:blank:]]\)\($$(BINDIR)\)|\1$$(DESTDIR)\2| ; \ s|\([[:blank:]]\)\($$(DATADIR)\)|\1$$(DESTDIR)\2| ; \ s|\(,\)\(@site_packages@\)|\1$$(DESTDIR)\2| ; \ s|\([[:blank:]]\)\(@site_packages@\)|\1$$(DESTDIR)\2|' \ ${WRKSRC}/Makefile.in post-install: @(${FIND} ${STAGEDIR}${PREFIX}/lib/Crux/lib -maxdepth 1 -type f \ -name "*.so" | ${XARGS} ${STRIP_CMD}) @(${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -maxdepth 3 -type f \ -name "*.so" | ${XARGS} ${STRIP_CMD}) .include Index: head/biology/plink/Makefile =================================================================== --- head/biology/plink/Makefile (revision 451981) +++ head/biology/plink/Makefile (revision 451982) @@ -1,27 +1,29 @@ # Created by: Jason Bacon # $FreeBSD$ PORTNAME= plink PORTVERSION= 1.07 PORTREVISION= 7 CATEGORIES= biology science MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ DISTNAME= ${PORTNAME}-${PORTVERSION}-src MAINTAINER= bacon4000@gmail.com COMMENT= Whole genome association analysis toolset +BROKEN= no public distfiles + LICENSE= GPLv2 LIB_DEPENDS= liblapack.so:math/lapack # We need Fortran LDFLAGS to link with Lapack. USES= fortran gmake zip PLIST_FILES= bin/plink do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/plink ${STAGEDIR}${PREFIX}/bin .include Index: head/biology/ssaha/Makefile =================================================================== --- head/biology/ssaha/Makefile (revision 451981) +++ head/biology/ssaha/Makefile (revision 451982) @@ -1,40 +1,42 @@ # Created by: Fernan Aguero # $FreeBSD$ PORTNAME= ssaha PORTVERSION= 3.1c PORTREVISION= 5 CATEGORIES= biology MASTER_SITES= ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha/ DISTNAME= ${PORTNAME}_v${PORTVERSION:S/.//} MAINTAINER= ports@FreeBSD.org COMMENT= Very fast matching and alignment of DNA sequences +BROKEN= No public distfiles + NO_WRKSUBDIR= yes BUILD_WRKSRC= ${WRKSRC}/Binary USES= gmake USE_GCC= any MAKE_ENV= CCC="${CXX}" OPTIM="${CXXFLAGS}" THREAD_LIB="-pthread" MAKEFILE= makefile ALL_TARGET= ssaha PLIST_FILES= bin/ssaha %%DATADIR%%/testSSAHA.csh \ ${DATA_FILES:S,^,%%DATADIR%%/,} DATA_FILES= test.fasta test_extract.fasta test_filter.fail \ test_filter.fastq test_protein.fasta README do-install: (cd ${BUILD_WRKSRC} && ${INSTALL_PROGRAM} ssaha \ ${STAGEDIR}${PREFIX}/bin) @${MKDIR} ${STAGEDIR}${DATADIR} (cd ${BUILD_WRKSRC} && ${INSTALL_SCRIPT} testSSAHA.csh \ ${STAGEDIR}${DATADIR}) .for i in ${DATA_FILES} (cd ${BUILD_WRKSRC} && ${INSTALL_DATA} ${i} \ ${STAGEDIR}${DATADIR}) .endfor .include Index: head/biology/tRNAscan-SE/Makefile =================================================================== --- head/biology/tRNAscan-SE/Makefile (revision 451981) +++ head/biology/tRNAscan-SE/Makefile (revision 451982) @@ -1,43 +1,45 @@ # Created by: chuynh@biolateral.com.au # $FreeBSD$ PORTNAME= tRNAscan-SE PORTVERSION= 1.23 PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/ MAINTAINER= ports@FreeBSD.org COMMENT= Improved tool for transfer RNA detection +BROKEN= No public distfiles + USES= perl5 tar:Z MAKE_ARGS= BINDIR="${PREFIX}/bin" \ LIBDIR="${DATADIR}" \ CC="${CC}" \ CFLAGS="${CFLAGS}" PLIST_FILES+= bin/covels-SE bin/coves-SE bin/eufindtRNA bin/tRNAscan-SE bin/trnascan-1.4 \ man/man1/tRNAscan-SE.1.gz PORTDATA= * PORTDOCS= Manual.ps OPTIONS_DEFINE= DOCS post-patch: @${REINPLACE_CMD} -e 's|tRNAscanSE setpaths|tRNAscanSE|g ; \ s|if tRNAscan-SE|if ./tRNAscan-SE|g' ${WRKSRC}/Makefile do-install: .for f in covels-SE coves-SE eufindtRNA trnascan-1.4 ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${STAGEDIR}${PREFIX}/bin .endfor ${INSTALL_SCRIPT} ${WRKSRC}/tRNAscan-SE ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/tRNAscan-SE.man ${STAGEDIR}${MANPREFIX}/man/man1/tRNAscan-SE.1 @${MKDIR} ${STAGEDIR}${DATADIR} .for f in TPCsignal Dsignal *.cm gcode.* ${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR} .endfor @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR} .include