Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 411784) +++ head/biology/Makefile (revision 411785) @@ -1,107 +1,108 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += jalview + SUBDIR += jellyfish SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-bioperl SUBDIR += p5-bioperl-run SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += platon SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += treeviewx SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/jellyfish/Makefile =================================================================== --- head/biology/jellyfish/Makefile (nonexistent) +++ head/biology/jellyfish/Makefile (revision 411785) @@ -0,0 +1,46 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= jellyfish +PORTVERSION= 2.2.4 +DISTVERSIONPREFIX= v +CATEGORIES= biology + +MAINTAINER= bacon4000@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 + +# 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 Property changes on: head/biology/jellyfish/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/distinfo =================================================================== --- head/biology/jellyfish/distinfo (nonexistent) +++ head/biology/jellyfish/distinfo (revision 411785) @@ -0,0 +1,2 @@ +SHA256 (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 44b6478aed63b859b8287d72b4f9bfb5d513fed334efbc8a9e5783da12ecb3ec +SIZE (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 658653 Property changes on: head/biology/jellyfish/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp =================================================================== --- head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp (nonexistent) +++ head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp (revision 411785) @@ -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 + #include + ++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 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(); Property changes on: head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/pkg-descr =================================================================== --- head/biology/jellyfish/pkg-descr (nonexistent) +++ head/biology/jellyfish/pkg-descr (revision 411785) @@ -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 Property changes on: head/biology/jellyfish/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/pkg-plist =================================================================== --- head/biology/jellyfish/pkg-plist (nonexistent) +++ head/biology/jellyfish/pkg-plist (revision 411785) @@ -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 Property changes on: head/biology/jellyfish/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property