FreeBSD Bugzilla – Attachment 168261 Details for
Bug 207929
[NEW PORT] biology/jellyfish: Fast, memory-efficient counting of k-mers in DNA
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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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Description:
Shar archive
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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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bug 207929
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