svn commit: r411785 - in head/biology: . jellyfish jellyfish/files
Dmitry Marakasov
amdmi3 at FreeBSD.org
Thu Mar 24 13:53:08 UTC 2016
Author: amdmi3
Date: Thu Mar 24 13:53:06 2016
New Revision: 411785
URL: https://svnweb.freebsd.org/changeset/ports/411785
Log:
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.
WWW: http://www.genome.umd.edu/jellyfish.html
PR: 207929
Submitted by: bacon4000 at gmail.com
Added:
head/biology/jellyfish/
head/biology/jellyfish/Makefile (contents, props changed)
head/biology/jellyfish/distinfo (contents, props changed)
head/biology/jellyfish/files/
head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp (contents, props changed)
head/biology/jellyfish/pkg-descr (contents, props changed)
head/biology/jellyfish/pkg-plist (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Thu Mar 24 13:35:32 2016 (r411784)
+++ head/biology/Makefile Thu Mar 24 13:53:06 2016 (r411785)
@@ -38,6 +38,7 @@
SUBDIR += htslib
SUBDIR += iolib
SUBDIR += jalview
+ SUBDIR += jellyfish
SUBDIR += lagan
SUBDIR += lamarc
SUBDIR += libgtextutils
Added: head/biology/jellyfish/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/jellyfish/Makefile Thu Mar 24 13:53:06 2016 (r411785)
@@ -0,0 +1,46 @@
+# Created by: Jason Bacon <bacon4000 at gmail.com>
+# $FreeBSD$
+
+PORTNAME= jellyfish
+PORTVERSION= 2.2.4
+DISTVERSIONPREFIX= v
+CATEGORIES= biology
+
+MAINTAINER= bacon4000 at gmail.com
+COMMENT= Fast, memory-efficient counting of k-mers in DNA
+
+LICENSE= GPLv3+
+LICENSE_FILE= ${WRKSRC}/LICENSE
+
+BUILD_DEPENDS= yaggo:${PORTSDIR}/devel/yaggo
+
+GNU_CONFIGURE= yes
+
+USES= autoreconf compiler:c++11-lib gmake \
+ libtool pkgconfig
+USE_LDCONFIG= yes
+
+USE_GITHUB= yes
+GH_ACCOUNT= gmarcais
+GH_PROJECT= Jellyfish
+
+INSTALL_TARGET= install-strip
+
+.include <bsd.port.pre.mk>
+
+# SSE code assumes amd64 features
+.if ${ARCH} != "amd64"
+.if ${OSVERSION} < 1000000
+IGNORE= multiple code issues on i386 < 10.0-RELEASE
+.else
+CONFIGURE_ARGS+=--without-sse
+.endif
+.endif
+
+# configure does not support --with-pkgconfigdir
+post-patch:
+ @${REINPLACE_CMD} \
+ -e 's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|g' \
+ ${WRKSRC}/Makefile.am
+
+.include <bsd.port.post.mk>
Added: head/biology/jellyfish/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/jellyfish/distinfo Thu Mar 24 13:53:06 2016 (r411785)
@@ -0,0 +1,2 @@
+SHA256 (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 44b6478aed63b859b8287d72b4f9bfb5d513fed334efbc8a9e5783da12ecb3ec
+SIZE (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 658653
Added: head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp Thu Mar 24 13:53:06 2016 (r411785)
@@ -0,0 +1,35 @@
+--- include/jellyfish/file_header.hpp.orig 2015-10-27 14:32:31 UTC
++++ include/jellyfish/file_header.hpp
+@@ -21,6 +21,8 @@
+ #include <jellyfish/generic_file_header.hpp>
+ #include <jellyfish/rectangular_binary_matrix.hpp>
+
++using std::string;
++
+ namespace jellyfish {
+ /// A header with jellyfish hash specific entries: size, matrix, etc.
+ class file_header : public generic_file_header {
+@@ -42,7 +44,10 @@ public:
+
+ RectangularBinaryMatrix matrix(int i = 1) const {
+ std::string name("matrix");
+- name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
++ char buff[100];
++ // name += std::to_string((long long int)i); // Cast to make gcc4.4 happy!
++ snprintf(buff, 99, "%d", i);
++ name += buff;
+ const unsigned int r = root_[name]["r"].asUInt();
+ const unsigned int c = root_[name]["c"].asUInt();
+ std::vector<uint64_t> raw(c, (uint64_t)0);
+@@ -53,7 +58,10 @@ public:
+
+ void matrix(const RectangularBinaryMatrix& m, int i = 1) {
+ std::string name("matrix");
+- name += std::to_string((long long int)i);
++ char buff[100];
++ // name += std::to_string((long long int)i);
++ snprintf(buff, 99, "%d", i);
++ name += buff;
+ root_[name].clear();
+ root_[name]["r"] = m.r();
+ root_[name]["c"] = m.c();
Added: head/biology/jellyfish/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/jellyfish/pkg-descr Thu Mar 24 13:53:06 2016 (r411785)
@@ -0,0 +1,7 @@
+Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
+A k-mer is a substring of length k, and counting the occurrences of all such
+substrings is a central step in many analyses of DNA sequence. JELLYFISH can
+count k-mers quickly by using an efficient encoding of a hash table and by
+exploiting the "compare-and-swap" CPU instruction to increase parallelism.
+
+WWW: http://www.genome.umd.edu/jellyfish.html
Added: head/biology/jellyfish/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/jellyfish/pkg-plist Thu Mar 24 13:53:06 2016 (r411785)
@@ -0,0 +1,55 @@
+bin/jellyfish
+include/jellyfish-2.2.4/jellyfish/allocators_mmap.hpp
+include/jellyfish-2.2.4/jellyfish/atomic_bits_array.hpp
+include/jellyfish-2.2.4/jellyfish/atomic_field.hpp
+include/jellyfish-2.2.4/jellyfish/atomic_gcc.hpp
+include/jellyfish-2.2.4/jellyfish/backtrace.hpp
+include/jellyfish-2.2.4/jellyfish/binary_dumper.hpp
+include/jellyfish-2.2.4/jellyfish/bloom_common.hpp
+include/jellyfish-2.2.4/jellyfish/bloom_counter2.hpp
+include/jellyfish-2.2.4/jellyfish/bloom_filter.hpp
+include/jellyfish-2.2.4/jellyfish/circular_buffer.hpp
+include/jellyfish-2.2.4/jellyfish/compare_and_swap.hpp
+include/jellyfish-2.2.4/jellyfish/cooperative_pool.hpp
+include/jellyfish-2.2.4/jellyfish/cooperative_pool2.hpp
+include/jellyfish-2.2.4/jellyfish/cpp_array.hpp
+include/jellyfish-2.2.4/jellyfish/divisor.hpp
+include/jellyfish-2.2.4/jellyfish/dumper.hpp
+include/jellyfish-2.2.4/jellyfish/err.hpp
+include/jellyfish-2.2.4/jellyfish/file_header.hpp
+include/jellyfish-2.2.4/jellyfish/generator_manager.hpp
+include/jellyfish-2.2.4/jellyfish/generic_file_header.hpp
+include/jellyfish-2.2.4/jellyfish/hash_counter.hpp
+include/jellyfish-2.2.4/jellyfish/int128.hpp
+include/jellyfish-2.2.4/jellyfish/jellyfish.hpp
+include/jellyfish-2.2.4/jellyfish/json.h
+include/jellyfish-2.2.4/jellyfish/large_hash_array.hpp
+include/jellyfish-2.2.4/jellyfish/large_hash_iterator.hpp
+include/jellyfish-2.2.4/jellyfish/locks_pthread.hpp
+include/jellyfish-2.2.4/jellyfish/mapped_file.hpp
+include/jellyfish-2.2.4/jellyfish/mer_dna.hpp
+include/jellyfish-2.2.4/jellyfish/mer_dna_bloom_counter.hpp
+include/jellyfish-2.2.4/jellyfish/mer_heap.hpp
+include/jellyfish-2.2.4/jellyfish/mer_iterator.hpp
+include/jellyfish-2.2.4/jellyfish/mer_overlap_sequence_parser.hpp
+include/jellyfish-2.2.4/jellyfish/mer_qual_iterator.hpp
+include/jellyfish-2.2.4/jellyfish/misc.hpp
+include/jellyfish-2.2.4/jellyfish/offsets_key_value.hpp
+include/jellyfish-2.2.4/jellyfish/rectangular_binary_matrix.hpp
+include/jellyfish-2.2.4/jellyfish/simple_circular_buffer.hpp
+include/jellyfish-2.2.4/jellyfish/sorted_dumper.hpp
+include/jellyfish-2.2.4/jellyfish/stdio_filebuf.hpp
+include/jellyfish-2.2.4/jellyfish/storage.hpp
+include/jellyfish-2.2.4/jellyfish/stream_iterator.hpp
+include/jellyfish-2.2.4/jellyfish/stream_manager.hpp
+include/jellyfish-2.2.4/jellyfish/text_dumper.hpp
+include/jellyfish-2.2.4/jellyfish/thread_exec.hpp
+include/jellyfish-2.2.4/jellyfish/time.hpp
+include/jellyfish-2.2.4/jellyfish/token_ring.hpp
+include/jellyfish-2.2.4/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
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