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