diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile index 42466adff130..d66105b1ba96 100644 --- a/biology/jellyfish/Makefile +++ b/biology/jellyfish/Makefile @@ -1,45 +1,46 @@ PORTNAME= Jellyfish DISTVERSIONPREFIX= v DISTVERSION= 2.3.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology MASTER_SITES= https://github.com/gmarcais/${PORTNAME}/releases/download/v2.3.0/ # Custom distfile reduces dependencies DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Fast, memory-efficient counting of k-mers in DNA WWW= http://www.genome.umd.edu/jellyfish.html LICENSE= BSD3CLAUSE GPLv3+ LICENSE_COMB= dual LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/LICENSE-BSD-3-Clause LICENSE_FILE_GPLv3+ = ${WRKSRC}/LICENSE-GPL-3.0 LIB_DEPENDS= libhts.so:biology/htslib USES= compiler:c++11-lib libtool USE_LDCONFIG= yes GNU_CONFIGURE= yes +GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share INSTALL_TARGET= install-strip PLIST_SUB= VER=${PORTVERSION} OPTIONS_DEFINE= NLS OPTIONS_SUB= yes NLS_USES= gettext NLS_CONFIGURE_ENABLE= nls .include # SSE code assumes amd64 features .if ${ARCH} != "amd64" CONFIGURE_ARGS+=--without-sse .endif .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -faligned-new .endif .include diff --git a/biology/jellyfish/pkg-plist b/biology/jellyfish/pkg-plist index 5ba3b5f5967b..c64b5673b696 100644 --- a/biology/jellyfish/pkg-plist +++ b/biology/jellyfish/pkg-plist @@ -1,57 +1,57 @@ bin/jellyfish include/jellyfish-%%VER%%/jellyfish/allocators_mmap.hpp include/jellyfish-%%VER%%/jellyfish/atomic_bits_array.hpp include/jellyfish-%%VER%%/jellyfish/atomic_field.hpp include/jellyfish-%%VER%%/jellyfish/atomic_gcc.hpp include/jellyfish-%%VER%%/jellyfish/backtrace.hpp include/jellyfish-%%VER%%/jellyfish/binary_dumper.hpp include/jellyfish-%%VER%%/jellyfish/bloom_common.hpp include/jellyfish-%%VER%%/jellyfish/bloom_counter2.hpp include/jellyfish-%%VER%%/jellyfish/bloom_filter.hpp include/jellyfish-%%VER%%/jellyfish/circular_buffer.hpp include/jellyfish-%%VER%%/jellyfish/compare_and_swap.hpp include/jellyfish-%%VER%%/jellyfish/cooperative_pool.hpp include/jellyfish-%%VER%%/jellyfish/cooperative_pool2.hpp include/jellyfish-%%VER%%/jellyfish/cpp_array.hpp include/jellyfish-%%VER%%/jellyfish/divisor.hpp include/jellyfish-%%VER%%/jellyfish/dumper.hpp include/jellyfish-%%VER%%/jellyfish/err.hpp include/jellyfish-%%VER%%/jellyfish/file_header.hpp include/jellyfish-%%VER%%/jellyfish/generator_manager.hpp include/jellyfish-%%VER%%/jellyfish/generic_file_header.hpp include/jellyfish-%%VER%%/jellyfish/hash_counter.hpp include/jellyfish-%%VER%%/jellyfish/int128.hpp include/jellyfish-%%VER%%/jellyfish/jellyfish.hpp include/jellyfish-%%VER%%/jellyfish/json.h include/jellyfish-%%VER%%/jellyfish/large_hash_array.hpp include/jellyfish-%%VER%%/jellyfish/large_hash_iterator.hpp include/jellyfish-%%VER%%/jellyfish/locks_pthread.hpp include/jellyfish-%%VER%%/jellyfish/mapped_file.hpp include/jellyfish-%%VER%%/jellyfish/mer_dna.hpp include/jellyfish-%%VER%%/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish-%%VER%%/jellyfish/mer_heap.hpp include/jellyfish-%%VER%%/jellyfish/mer_iterator.hpp include/jellyfish-%%VER%%/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish-%%VER%%/jellyfish/mer_qual_iterator.hpp include/jellyfish-%%VER%%/jellyfish/misc.hpp include/jellyfish-%%VER%%/jellyfish/offsets_key_value.hpp include/jellyfish-%%VER%%/jellyfish/parser_common.hpp include/jellyfish-%%VER%%/jellyfish/rectangular_binary_matrix.hpp include/jellyfish-%%VER%%/jellyfish/sam_format.hpp include/jellyfish-%%VER%%/jellyfish/simple_circular_buffer.hpp include/jellyfish-%%VER%%/jellyfish/sorted_dumper.hpp include/jellyfish-%%VER%%/jellyfish/stdio_filebuf.hpp include/jellyfish-%%VER%%/jellyfish/storage.hpp include/jellyfish-%%VER%%/jellyfish/stream_iterator.hpp include/jellyfish-%%VER%%/jellyfish/stream_manager.hpp include/jellyfish-%%VER%%/jellyfish/text_dumper.hpp include/jellyfish-%%VER%%/jellyfish/thread_exec.hpp include/jellyfish-%%VER%%/jellyfish/time.hpp include/jellyfish-%%VER%%/jellyfish/token_ring.hpp include/jellyfish-%%VER%%/jellyfish/whole_sequence_parser.hpp lib/libjellyfish-2.0.a lib/libjellyfish-2.0.so lib/libjellyfish-2.0.so.2 lib/libjellyfish-2.0.so.2.0.0 libdata/pkgconfig/jellyfish-2.0.pc -man/man1/jellyfish.1.gz +share/man/man1/jellyfish.1.gz