Attachment 168261 Details for Bug 207929 – Shar archive

Shar archive

jellyfish-shar.txt (text/plain), 6.75 KB, created by Jason W. Bacon on 2016-03-15 21:18:13 UTC

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Creator: Jason W. Bacon

Created: 2016-03-15 21:18:13 UTC

Size: 6.75 KB

patch

obsolete

># This is a shell archive.  Save it in a file, remove anything before
># this line, and then unpack it by entering "sh file".  Note, it may
># create directories; files and directories will be owned by you and
># have default permissions.
>#
># This archive contains:
>#
>#	jellyfish
>#	jellyfish/Makefile
>#	jellyfish/distinfo
>#	jellyfish/pkg-descr
>#	jellyfish/pkg-plist
>#	jellyfish/files
>#	jellyfish/files/patch-include_jellyfish_file__header.hpp
>#
>echo c - jellyfish
>mkdir -p jellyfish > /dev/null 2>&1
>echo x - jellyfish/Makefile
>sed 's/^X//' >jellyfish/Makefile << '7f460199a746594927722190e1c7488c'
>X# Created by: Jason Bacon <bacon4000@gmail.com>
>X# $FreeBSD$
>X
>XPORTNAME=		jellyfish
>XPORTVERSION=		2.2.4
>XDISTVERSIONPREFIX=	v
>XCATEGORIES=		biology
>X
>XMAINTAINER=	bacon4000@gmail.com
>XCOMMENT=	Fast, memory-efficient counting of k-mers in DNA
>X
>XLICENSE=	GPLv3
>X
>XBUILD_DEPENDS+=	yaggo:${PORTSDIR}/devel/yaggo
>X
>XGNU_CONFIGURE=	yes
>X
>XUSES=		autoreconf compiler:c++11-lib compiler:openmp gmake \
>X		libtool pkgconfig
>XUSE_LDCONFIG=	yes
>X
>XUSE_GITHUB=	yes
>XGH_ACCOUNT=	gmarcais
>XGH_PROJECT=	Jellyfish
>X
>XINSTALL_TARGET=	install-strip
>X
>X.include <bsd.port.pre.mk>
>X
>X# SSE code assumes amd64 features
>X.if ${ARCH} != "amd64"
>X.if ${OSVERSION} < 1000000
>XIGNORE=		multiple code issues on i386 < 10.0-RELEASE
>X.else
>XCONFIGURE_ARGS=	--without-sse
>X.endif
>X.endif
>X
>X# configure does not support --with-pkgconfigdir
>Xpost-patch:
>X	${REINPLACE_CMD} \
>X		-e 's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|g' \
>X		${WRKSRC}/Makefile.am
>X
>X.include <bsd.port.post.mk>
>7f460199a746594927722190e1c7488c
>echo x - jellyfish/distinfo
>sed 's/^X//' >jellyfish/distinfo << 'd87e04139ae4e74bc16fc9030ed0dd81'
>XSHA256 (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 44b6478aed63b859b8287d72b4f9bfb5d513fed334efbc8a9e5783da12ecb3ec
>XSIZE (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 658653
>d87e04139ae4e74bc16fc9030ed0dd81
>echo x - jellyfish/pkg-descr
>sed 's/^X//' >jellyfish/pkg-descr << 'c0d0864fdd0f5290ac82676bf44f990d'
>XJellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
>XA k-mer is a substring of length k, and counting the occurrences of all such
>Xsubstrings is a central step in many analyses of DNA sequence. JELLYFISH can
>Xcount k-mers quickly by using an efficient encoding of a hash table and by
>Xexploiting the "compare-and-swap" CPU instruction to increase parallelism.
>X
>XWWW: http://www.genome.umd.edu/jellyfish.html
>c0d0864fdd0f5290ac82676bf44f990d
>echo x - jellyfish/pkg-plist
>sed 's/^X//' >jellyfish/pkg-plist << 'e7be169d819c973777b29429537f26be'
>Xbin/jellyfish
>Xinclude/jellyfish-2.2.4/jellyfish/allocators_mmap.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/atomic_bits_array.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/atomic_field.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/atomic_gcc.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/backtrace.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/binary_dumper.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/bloom_common.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/bloom_counter2.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/bloom_filter.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/circular_buffer.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/compare_and_swap.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/cooperative_pool.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/cooperative_pool2.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/cpp_array.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/divisor.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/dumper.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/err.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/file_header.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/generator_manager.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/generic_file_header.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/hash_counter.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/int128.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/jellyfish.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/json.h
>Xinclude/jellyfish-2.2.4/jellyfish/large_hash_array.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/large_hash_iterator.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/locks_pthread.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mapped_file.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mer_dna.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mer_dna_bloom_counter.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mer_heap.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mer_iterator.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mer_overlap_sequence_parser.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/mer_qual_iterator.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/misc.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/offsets_key_value.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/rectangular_binary_matrix.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/simple_circular_buffer.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/sorted_dumper.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/stdio_filebuf.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/storage.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/stream_iterator.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/stream_manager.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/text_dumper.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/thread_exec.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/time.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/token_ring.hpp
>Xinclude/jellyfish-2.2.4/jellyfish/whole_sequence_parser.hpp
>Xlib/libjellyfish-2.0.a
>Xlib/libjellyfish-2.0.so
>Xlib/libjellyfish-2.0.so.2
>Xlib/libjellyfish-2.0.so.2.0.0
>Xlibdata/pkgconfig/jellyfish-2.0.pc
>Xman/man1/jellyfish.1.gz
>e7be169d819c973777b29429537f26be
>echo c - jellyfish/files
>mkdir -p jellyfish/files > /dev/null 2>&1
>echo x - jellyfish/files/patch-include_jellyfish_file__header.hpp
>sed 's/^X//' >jellyfish/files/patch-include_jellyfish_file__header.hpp << 'e043b45438f46fe728df536edddfd922'
>X--- include/jellyfish/file_header.hpp.orig	2015-10-27 14:32:31 UTC
>X+++ include/jellyfish/file_header.hpp
>X@@ -21,6 +21,8 @@
>X #include <jellyfish/generic_file_header.hpp>
>X #include <jellyfish/rectangular_binary_matrix.hpp>
>X 
>X+using std::string;
>X+
>X namespace jellyfish {
>X /// A header with jellyfish hash specific entries: size, matrix, etc.
>X class file_header : public generic_file_header {
>X@@ -42,7 +44,10 @@ public:
>X 
>X   RectangularBinaryMatrix matrix(int i = 1) const {
>X     std::string name("matrix");
>X-    name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
>X+    char   buff[100];
>X+    // name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
>X+    snprintf(buff, 99, "%d", i);
>X+    name += buff;
>X     const unsigned int r = root_[name]["r"].asUInt();
>X     const unsigned int c = root_[name]["c"].asUInt();
>X     std::vector<uint64_t> raw(c, (uint64_t)0);
>X@@ -53,7 +58,10 @@ public:
>X 
>X   void matrix(const RectangularBinaryMatrix& m, int i = 1) {
>X     std::string name("matrix");
>X-    name += std::to_string((long long int)i);
>X+    char   buff[100];
>X+    // name += std::to_string((long long int)i);
>X+    snprintf(buff, 99, "%d", i);
>X+    name += buff;
>X     root_[name].clear();
>X     root_[name]["r"] = m.r();
>X     root_[name]["c"] = m.c();
>e043b45438f46fe728df536edddfd922
>exit
>

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rakuco: maintainer-approval+

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Attachments on bug 207929: 168261