diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index 5cd99f2c632b..75af10326376 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -1,78 +1,80 @@ PORTNAME= libsbml PORTVERSION= 5.21.0 DISTVERSIONPREFIX= v CATEGORIES= biology devel MAINTAINER= sunpoet@FreeBSD.org COMMENT= API Library for Working with SBML File WWW= https://sbml.org/software/libsbml/ \ https://synonym.caltech.edu/ \ https://github.com/sbmlteam/libsbml LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.txt -USES= cmake:testing iconv:build +USES= cmake:testing cpe iconv:build CMAKE_OFF= EXIT_ON_ERROR \ LIBSBML_SKIP_SHARED_LIBRARY \ LIBSBML_SKIP_STATIC_LIBRARY \ LIBSBML_USE_STRICT_INCLUDES \ PYTHON_USE_API2_WARNINGS \ WITH_ALL_PACKAGES \ WITH_CHECK \ WITH_CPP_NAMESPACE \ WITH_CSHARP \ WITH_DOXYGEN \ WITH_JAVA \ WITH_JAVASCRIPT \ WITH_MATLAB \ WITH_OCTAVE \ WITH_PERL \ WITH_PHP \ WITH_R \ WITH_STABLE_PACKAGES \ WITH_WALL CMAKE_ON= LIBSBML_SHARED_VERSION \ WITH_BZIP2 \ WITH_SWIG \ WITH_THREADSAFE_PARSER \ WITH_ZLIB CMAKE_TESTING_ON= WITH_CHECK USE_CXXSTD= c++98 USE_LDCONFIG= yes PLIST_SUB= PORTVERSION=${PORTVERSION} USE_GITHUB= yes GH_ACCOUNT= sbmlteam OPTIONS_DEFINE= EXAMPLES PYTHON RUBY OPTIONS_SINGLE= XML OPTIONS_SINGLE_XML= EXPAT LIBXML2 XERCES OPTIONS_DEFAULT=LIBXML2 PYTHON OPTIONS_SUB= yes EXAMPLES_CMAKE_BOOL= WITH_EXAMPLES EXPAT_CMAKE_BOOL= WITH_EXPAT EXPAT_LIB_DEPENDS= libexpat.so:textproc/expat2 LIBXML2_CMAKE_BOOL= WITH_LIBXML LIBXML2_USE= GNOME=libxml2 LIBXML2_USES= gnome PYTHON_BUILD_DEPENDS= swig:devel/swig PYTHON_CMAKE_BOOL= WITH_PYTHON PYTHON_USES= python PYTHON_CMAKE_ON= WITH_SWIG RUBY_BUILD_DEPENDS= swig:devel/swig RUBY_CMAKE_BOOL= WITH_RUBY RUBY_USES= ruby XERCES_CMAKE_BOOL= WITH_XERCES XERCES_LIB_DEPENDS= libxerces-c.so:textproc/xerces-c3 +CPE_VENDOR= ${PORTNAME}_project + post-patch: @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt post-install-EXAMPLES-on: ${MV} ${STAGEDIR}${DATADIR}examples ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile index 8b38c60021ae..53389082d07d 100644 --- a/biology/samtools/Makefile +++ b/biology/samtools/Makefile @@ -1,29 +1,31 @@ PORTNAME= samtools DISTVERSION= 1.23.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for manipulating next-generation sequencing data WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.22:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash -USES= autoreconf gmake localbase ncurses perl5 python:env shebangfix +USES= autoreconf cpe gmake localbase ncurses perl5 python:env shebangfix USE_GITHUB= yes USE_PERL5= test GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl CONFIGURE_ARGS= --with-htslib=system TEST_TARGET= test +CPE_VENDOR= htslib + .include