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head/biology/bcftools/Makefile
| # Created by: Reed A. Cartwright <cartwright@asu.edu> | # Created by: Reed A. Cartwright <cartwright@asu.edu> | ||||
| # $FreeBSD$ | # $FreeBSD$ | ||||
| PORTNAME= bcftools | PORTNAME= bcftools | ||||
| PORTVERSION= 1.6 | PORTVERSION= 1.9 | ||||
| PORTREVISION= 1 | |||||
| CATEGORIES= biology | CATEGORIES= biology | ||||
| MAINTAINER= cartwright@asu.edu | MAINTAINER= cartwright@asu.edu | ||||
| COMMENT= Tools for manipulating next-generation sequencing data | COMMENT= Tools for manipulating next-generation sequencing data | ||||
| LICENSE= MIT | LICENSE= MIT | ||||
| # LICENSE_FILE= ${WRKSRC}/LICENSE | LICENSE_FILE= ${WRKSRC}/LICENSE | ||||
| BUILD_DEPENDS= htslib>=1.6:biology/htslib | BUILD_DEPENDS= htslib>=1.6:biology/htslib | ||||
| LIB_DEPENDS= libhts.so:biology/htslib | LIB_DEPENDS= libhts.so:biology/htslib | ||||
| TEST_DEPENDS= bash:shells/bash | TEST_DEPENDS= bash:shells/bash | ||||
| CONFLICTS_BUILD=openssl | CONFLICTS_BUILD=openssl | ||||
| USES= autoreconf gmake localbase \ | |||||
| perl5 python:env shebangfix | |||||
| USE_GITHUB= yes | USE_GITHUB= yes | ||||
| GH_ACCOUNT= samtools | GH_ACCOUNT= samtools | ||||
| USES= autoreconf gmake perl5 python:env shebangfix | USE_LDCONFIG= ${PREFIX}/libexec/${PORTNAME} | ||||
| USE_PERL5= test | USE_PERL5= test | ||||
| GNU_CONFIGURE= yes | GNU_CONFIGURE= yes | ||||
| SUB_FILES= pkg-message | |||||
| SHEBANG_FILES= misc/* test/test.pl | SHEBANG_FILES= misc/* test/test.pl | ||||
| OPTIONS_DEFINE= GPL | OPTIONS_DEFINE= GPL | ||||
| GPL_DESC= Enable modules that rely on GPL code | GPL_DESC= Enable modules that rely on GPL code | ||||
| OPTIONS_DEFAULT= GPL | OPTIONS_DEFAULT= GPL | ||||
| GPL_LIB_DEPENDS= libgsl.so:math/gsl | GPL_LIB_DEPENDS= libgsl.so:math/gsl | ||||
| .include <bsd.port.options.mk> | .include <bsd.port.options.mk> | ||||
| CPPFLAGS+= -I${LOCALBASE}/include | |||||
| LDFLAGS+= -L${LOCALBASE}/lib | |||||
| .if ${PORT_OPTIONS:MGPL} | .if ${PORT_OPTIONS:MGPL} | ||||
| MAKE_ENV+= USE_GPL=1 | MAKE_ENV+= USE_GPL=1 | ||||
| LICENSE= GPLv3 | LICENSE+= GPLv3 | ||||
| LICENSE_COMB= multi | |||||
| .endif | .endif | ||||
| TEST_TARGET= test | TEST_TARGET= test | ||||
| post-patch: | post-patch: | ||||
| @${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1) | |||||
| @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac | @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac | ||||
| post-install: | |||||
| ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \ | |||||
| ${STAGEDIR}${PREFIX}/bin/color-chrs | |||||
| ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\ | |||||
| ${STAGEDIR}${PREFIX}/bin/guess-ploidy | |||||
| ${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \ | |||||
| ${STAGEDIR}${PREFIX}/bin/plot-roh | |||||
| ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \ | |||||
| ${STAGEDIR}${PREFIX}/bin/run-roh | |||||
| ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \ | |||||
| ${STAGEDIR}${PREFIX}/bin/vcfutils | |||||
| ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \ | |||||
| ${STAGEDIR}${PREFIX}/bin/ | |||||
| ${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/ | |||||
| .include <bsd.port.mk> | .include <bsd.port.mk> | ||||