diff options
Diffstat (limited to 'biology/salmon/Makefile')
| -rw-r--r-- | biology/salmon/Makefile | 26 |
1 files changed, 17 insertions, 9 deletions
diff --git a/biology/salmon/Makefile b/biology/salmon/Makefile index 74631d470a17..8332ba416d74 100644 --- a/biology/salmon/Makefile +++ b/biology/salmon/Makefile @@ -1,7 +1,6 @@ PORTNAME= salmon DISTVERSIONPREFIX= v -DISTVERSION= 1.10.2 -PORTREVISION= 8 +DISTVERSION= 1.10.3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -20,18 +19,23 @@ BUILD_DEPENDS= bash:shells/bash \ libgff==2.0.0:biology/libgff \ libtool:devel/libtool \ autoreconf:devel/autoconf \ - aclocal:devel/automake -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ - libtbb.so:devel/onetbb \ - libcurl.so:ftp/curl + aclocal:devel/automake \ + eigen>0:math/eigen3 \ + libdivide>0:math/libdivide \ + curl>0:ftp/curl +LIB_DEPENDS= libtbb.so:devel/onetbb USES= cmake:noninja gmake localbase shebangfix USE_GITHUB= yes +# Can't unbundle io_lib unless we also unbundle htscodecs from io_lib, +# which is a nightmare: explicitly integrated into configure files and +# installs htscodecs files, conflicting with separate htscodecs port. GH_ACCOUNT= COMBINE-lab -GH_TUPLE+= COMBINE-lab:pufferfish:salmon-v1.10.2:pf/external/pufferfish -GH_TUPLE+= jkbonfield:io_lib:io_lib-1-14-15:sio/external/staden-io_lib -GH_TUPLE+= samtools:htscodecs:5aecc6e:htscodec/external/staden-io_lib/htscodecs +GH_TUPLE+= COMBINE-lab:pufferfish:salmon-v${DISTVERSION}:pf/external/pufferfish +GH_TUPLE+= jkbonfield:io_lib:io_lib-1-15-1:sio/external/staden-io_lib +# Update commit hash from io_lib release branch +GH_TUPLE+= samtools:htscodecs:de42211:htscodec/external/staden-io_lib/htscodecs SHEBANG_FILES= scripts/* PLIST_FILES= bin/salmon @@ -40,9 +44,13 @@ CMAKE_ARGS+= -DHAVE_FAST_MALLOC:BOOL=on \ -DFETCHED_PUFFERFISH:BOOL=on \ -DFETCHED_LIBGFF:BOOL=on \ -DFETCH_STADEN:BOOL=true +WITH_DEBUG= yes +CXXFLAGS+= -I${LOCALBASE}/include/eigen3 LDFLAGS+= -lpthread pre-configure: + ${RM} -rf ${WRKSRC}/include/eigen3 \ + ${WRKSRC}/external/pufferfish/include/libdivide (cd ${WRKSRC}/external/staden-io_lib && ./bootstrap) do-install: |