cf5d9b8b96
and bump dependent ports' revisions. Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.11.0
52 lines
1.5 KiB
Makefile
52 lines
1.5 KiB
Makefile
PORTNAME= salmon
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.10.2
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PORTREVISION= 2
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Transcript-level quantification of RNA-seq from lightweight alignments
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WWW= https://github.com/COMBINE-lab/salmon
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LICENSE= GPLv3
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LICENSE_FILE= ${WRKSRC}/LICENSE
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NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc powerpcspe
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NOT_FOR_ARCHS_REASON= Requires 64-bit processor
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# libtool and auto* are run manually in submodules, so don't put them in USES
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BUILD_DEPENDS= bash:shells/bash \
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cereal>=1.3.0:devel/cereal \
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libgff==2.0.0:biology/libgff \
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libtool:devel/libtool \
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autoreconf:devel/autoconf \
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aclocal:devel/automake
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LIB_DEPENDS= libboost_system.so:devel/boost-libs \
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libtbb.so:devel/onetbb \
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libcurl.so:ftp/curl
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USES= cmake:noninja gmake localbase shebangfix
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USE_GITHUB= yes
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GH_ACCOUNT= COMBINE-lab
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GH_TUPLE+= COMBINE-lab:pufferfish:salmon-v1.10.2:pf/external/pufferfish
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GH_TUPLE+= jkbonfield:io_lib:io_lib-1-14-15:sio/external/staden-io_lib
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GH_TUPLE+= samtools:htscodecs:5aecc6e:htscodec/external/staden-io_lib/htscodecs
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SHEBANG_FILES= scripts/*
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PLIST_FILES= bin/salmon
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CMAKE_ARGS+= -DHAVE_FAST_MALLOC:BOOL=on \
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-DBOOST_ROOT:PATH=${LOCALBASE} \
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-DFETCHED_PUFFERFISH:BOOL=on \
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-DFETCHED_LIBGFF:BOOL=on \
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-DFETCH_STADEN:BOOL=true
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WITH_DEBUG= yes
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LDFLAGS+= -lpthread
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pre-configure:
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(cd ${WRKSRC}/external/staden-io_lib && ./bootstrap)
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do-install:
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${INSTALL_PROGRAM} ${BUILD_WRKSRC}/src/salmon ${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.mk>
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