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Import jellyfish-2.2.0 as wip/jellyfish2.
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Tue May 10 21:44:45 2016 -0500
Changeset: d71018f3dd7a4be6a8fdb0514efb971087525d7a
Added Files:
jellyfish2/DESCR
jellyfish2/Makefile
jellyfish2/PLIST
jellyfish2/TODO
jellyfish2/distinfo
jellyfish2/patches/patch-include_jellyfish_file__header.hpp
Log Message:
Import jellyfish-2.2.0 as wip/jellyfish2.
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.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d71018f3dd7a4be6a8fdb0514efb971087525d7a
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
jellyfish2/DESCR | 5 ++
jellyfish2/Makefile | 59 ++++++++++++++++++++++
jellyfish2/PLIST | 53 +++++++++++++++++++
jellyfish2/TODO | 1 +
jellyfish2/distinfo | 5 ++
.../patch-include_jellyfish_file__header.hpp | 37 ++++++++++++++
6 files changed, 160 insertions(+)
diffs:
diff --git a/jellyfish2/DESCR b/jellyfish2/DESCR
new file mode 100644
index 0000000..4b5859e
--- /dev/null
+++ b/jellyfish2/DESCR
@@ -0,0 +1,5 @@
+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.
diff --git a/jellyfish2/Makefile b/jellyfish2/Makefile
new file mode 100644
index 0000000..a88d8d9
--- /dev/null
+++ b/jellyfish2/Makefile
@@ -0,0 +1,59 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+## Created by: Jason Bacon <bacon4000%gmail.com@localhost>
+## $FreeBSD$
+#USE_LDCONFIG= yes
+#post-stage:
+# ${MV} ${DESTDIR}${PREFIX}/lib/pkgconfig/* \
+# ${DESTDIR}${PREFIX}/libdata/pkgconfig
+#.include <bsd.port.mk>
+
+DISTNAME= jellyfish-${PORTVERSION}
+CATEGORIES= biology
+MASTER_SITES= ftp://ftp.genome.umd.edu/pub/jellyfish/
+
+MAINTAINER= dsiercks%uwm.edu@localhost
+HOMEPAGE= http://www.genome.umd.edu/jellyfish.html
+COMMENT= Fast, memory-efficient counting of k-mers in DNA
+# Check this
+LICENSE= gnu-gpl-v3
+
+# FIXME: Only for amd64
+# Test and change if necessary.
+# MAKE_JOBS_SAFE= no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES= c c++
+USE_LIBTOOL= yes
+GNU_CONFIGURE= yes
+
+CFLAGS= -fopenmp
+
+CXXFLAGS+= -std=c++0x
+
+FFLAGS= -fopenmp
+
+PORTVERSION= 2.2.0
+DATADIR= ${PREFIX}/share/jellyfish
+DOCSDIR= ${PREFIX}/share/doc/jellyfish
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+# Keep this if there are user-selectable options.
+# .include "options.mk"
+
+# Specify which directories to create before install.
+# You should only need this if using your own install target.
+INSTALLATION_DIRS= bin lib ${PKGMANDIR}/man1 share/doc share/examples
+
+# Linux doesn't have zlib in the base, so just in case...
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/jellyfish2/PLIST b/jellyfish2/PLIST
new file mode 100644
index 0000000..33ef5ef
--- /dev/null
+++ b/jellyfish2/PLIST
@@ -0,0 +1,53 @@
+@comment $NetBSD$
+bin/jellyfish
+include/${PKGNAME}/jellyfish/allocators_mmap.hpp
+include/${PKGNAME}/jellyfish/atomic_bits_array.hpp
+include/${PKGNAME}/jellyfish/atomic_field.hpp
+include/${PKGNAME}/jellyfish/atomic_gcc.hpp
+include/${PKGNAME}/jellyfish/backtrace.hpp
+include/${PKGNAME}/jellyfish/binary_dumper.hpp
+include/${PKGNAME}/jellyfish/bloom_common.hpp
+include/${PKGNAME}/jellyfish/bloom_counter2.hpp
+include/${PKGNAME}/jellyfish/bloom_filter.hpp
+include/${PKGNAME}/jellyfish/circular_buffer.hpp
+include/${PKGNAME}/jellyfish/compare_and_swap.hpp
+include/${PKGNAME}/jellyfish/cooperative_pool2.hpp
+include/${PKGNAME}/jellyfish/cooperative_pool.hpp
+include/${PKGNAME}/jellyfish/cpp_array.hpp
+include/${PKGNAME}/jellyfish/divisor.hpp
+include/${PKGNAME}/jellyfish/dumper.hpp
+include/${PKGNAME}/jellyfish/err.hpp
+include/${PKGNAME}/jellyfish/file_header.hpp
+include/${PKGNAME}/jellyfish/generator_manager.hpp
+include/${PKGNAME}/jellyfish/generic_file_header.hpp
+include/${PKGNAME}/jellyfish/hash_counter.hpp
+include/${PKGNAME}/jellyfish/int128.hpp
+include/${PKGNAME}/jellyfish/jellyfish.hpp
+include/${PKGNAME}/jellyfish/json.h
+include/${PKGNAME}/jellyfish/large_hash_array.hpp
+include/${PKGNAME}/jellyfish/large_hash_iterator.hpp
+include/${PKGNAME}/jellyfish/locks_pthread.hpp
+include/${PKGNAME}/jellyfish/mapped_file.hpp
+include/${PKGNAME}/jellyfish/mer_dna_bloom_counter.hpp
+include/${PKGNAME}/jellyfish/mer_dna.hpp
+include/${PKGNAME}/jellyfish/mer_heap.hpp
+include/${PKGNAME}/jellyfish/mer_iterator.hpp
+include/${PKGNAME}/jellyfish/mer_overlap_sequence_parser.hpp
+include/${PKGNAME}/jellyfish/mer_qual_iterator.hpp
+include/${PKGNAME}/jellyfish/misc.hpp
+include/${PKGNAME}/jellyfish/offsets_key_value.hpp
+include/${PKGNAME}/jellyfish/rectangular_binary_matrix.hpp
+include/${PKGNAME}/jellyfish/simple_circular_buffer.hpp
+include/${PKGNAME}/jellyfish/sorted_dumper.hpp
+include/${PKGNAME}/jellyfish/stdio_filebuf.hpp
+include/${PKGNAME}/jellyfish/storage.hpp
+include/${PKGNAME}/jellyfish/stream_iterator.hpp
+include/${PKGNAME}/jellyfish/stream_manager.hpp
+include/${PKGNAME}/jellyfish/text_dumper.hpp
+include/${PKGNAME}/jellyfish/thread_exec.hpp
+include/${PKGNAME}/jellyfish/time.hpp
+include/${PKGNAME}/jellyfish/token_ring.hpp
+include/${PKGNAME}/jellyfish/whole_sequence_parser.hpp
+lib/libjellyfish-2.0.la
+lib/pkgconfig/jellyfish-2.0.pc
+man/man1/jellyfish.1
diff --git a/jellyfish2/TODO b/jellyfish2/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/jellyfish2/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/jellyfish2/distinfo b/jellyfish2/distinfo
new file mode 100644
index 0000000..f44555f
--- /dev/null
+++ b/jellyfish2/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+SHA1 (jellyfish-2.2.0.tar.gz) = 9ac4817aed0c61a1819b913193b0e312fa4fa9bd
+RMD160 (jellyfish-2.2.0.tar.gz) = 01e5847c72bf1bf92989b1158988605b1155aec4
+Size (jellyfish-2.2.0.tar.gz) = 1085913 bytes
diff --git a/jellyfish2/patches/patch-include_jellyfish_file__header.hpp b/jellyfish2/patches/patch-include_jellyfish_file__header.hpp
new file mode 100644
index 0000000..9dca771
--- /dev/null
+++ b/jellyfish2/patches/patch-include_jellyfish_file__header.hpp
@@ -0,0 +1,37 @@
+$NetBSD$
+
+--- include/jellyfish/file_header.hpp.orig 2013-12-13 19:04:16 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();
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