Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 501146) +++ head/biology/Makefile (revision 501147) @@ -1,163 +1,164 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO 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-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet + SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/vsearch/Makefile =================================================================== --- head/biology/vsearch/Makefile (nonexistent) +++ head/biology/vsearch/Makefile (revision 501147) @@ -0,0 +1,32 @@ +# $FreeBSD$ + +PORTNAME= vsearch +DISTVERSIONPREFIX= v +DISTVERSION= 2.13.3 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Versatile open-source tool for metagenomics + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +# Note: For PPC need power8 or later, little endian +ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 +ONLY_FOR_ARCHS_REASON= Explicitly enumerated by upstream developers + +LIB_DEPENDS= libsysinfo.so:devel/libsysinfo + +USES= autoreconf gmake localbase +USE_GITHUB= yes + +GH_ACCOUNT= torognes +GNU_CONFIGURE= yes + +PLIST_FILES= bin/vsearch man/man1/vsearch.1.gz +PORTDOCS= * + +OPTIONS_DEFINE= DOCS +OPTIONS_SUB= yes + +.include Property changes on: head/biology/vsearch/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/vsearch/distinfo =================================================================== --- head/biology/vsearch/distinfo (nonexistent) +++ head/biology/vsearch/distinfo (revision 501147) @@ -0,0 +1,3 @@ +TIMESTAMP = 1557339663 +SHA256 (torognes-vsearch-v2.13.3_GH0.tar.gz) = e5f34ece28b76403d3ba4a673eca41178fe399c35a1023dbc87d0c0da5efaa52 +SIZE (torognes-vsearch-v2.13.3_GH0.tar.gz) = 233846 Property changes on: head/biology/vsearch/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/vsearch/files/patch-configure.ac =================================================================== --- head/biology/vsearch/files/patch-configure.ac (nonexistent) +++ head/biology/vsearch/files/patch-configure.ac (revision 501147) @@ -0,0 +1,12 @@ +--- configure.ac.orig 2019-05-09 20:58:52 UTC ++++ configure.ac +@@ -14,9 +14,6 @@ MACOSX_DEPLOYMENT_TARGET="10.9" + + # Set default gcc and g++ options + +-CFLAGS='-g' +-CXXFLAGS='-g' +- + # Checks for programs. + AC_PROG_CXX + AC_PROG_RANLIB Property changes on: head/biology/vsearch/files/patch-configure.ac ___________________________________________________________________ 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/vsearch/files/patch-src_Makefile.am =================================================================== --- head/biology/vsearch/files/patch-src_Makefile.am (nonexistent) +++ head/biology/vsearch/files/patch-src_Makefile.am (revision 501147) @@ -0,0 +1,18 @@ +--- src/Makefile.am.orig 2019-04-30 11:57:32 UTC ++++ src/Makefile.am +@@ -1,12 +1,12 @@ + bin_PROGRAMS = $(top_builddir)/bin/vsearch + + if TARGET_PPC +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8 ++AM_CXXFLAGS=-Wall -Wsign-compare + else + if TARGET_AARCH64 +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic ++AM_CXXFLAGS=-Wall -Wsign-compare + else +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic ++AM_CXXFLAGS=-Wall -Wsign-compare + endif + endif + Property changes on: head/biology/vsearch/files/patch-src_Makefile.am ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/vsearch/files/patch-src_city.cc =================================================================== --- head/biology/vsearch/files/patch-src_city.cc (nonexistent) +++ head/biology/vsearch/files/patch-src_city.cc (revision 501147) @@ -0,0 +1,20 @@ +$NetBSD$ + +# Portability + +--- src/city.cc.orig 2019-04-30 11:57:32 UTC ++++ src/city.cc +@@ -60,6 +60,13 @@ static uint32 UNALIGNED_LOAD32(const char *p) { + #define bswap_32(x) OSSwapInt32(x) + #define bswap_64(x) OSSwapInt64(x) + ++#elif defined(__FreeBSD__) ++ ++#include ++ ++#define bswap_32(x) bswap32(x) ++#define bswap_64(x) bswap64(x) ++ + #elif defined(__NetBSD__) + + #include Property changes on: head/biology/vsearch/files/patch-src_city.cc ___________________________________________________________________ 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/vsearch/files/patch-src_vsearch.h =================================================================== --- head/biology/vsearch/files/patch-src_vsearch.h (nonexistent) +++ head/biology/vsearch/files/patch-src_vsearch.h (revision 501147) @@ -0,0 +1,67 @@ +$NetBSD$ + +# Add FreeBSD and NetBSD support + +--- src/vsearch.h.orig 2019-04-30 11:57:32 UTC ++++ src/vsearch.h +@@ -138,30 +138,50 @@ + #define bswap_32(x) _byteswap_ulong(x) + #define bswap_64(x) _byteswap_uint64(x) + +-#else ++#elif defined(__APPLE__) + +-#ifdef __APPLE__ +- + #define PROG_OS "macos" + #include + #include ++#include + #define bswap_16(x) OSSwapInt16(x) + #define bswap_32(x) OSSwapInt32(x) + #define bswap_64(x) OSSwapInt64(x) + +-#else ++#elif defined(__linux__) + +-#ifdef __linux__ + #define PROG_OS "linux" +-#else +-#define PROG_OS "unknown" +-#endif +- + #include + #include ++#include + +-#endif ++#elif defined(__FreeBSD__) + ++#define PROG_OS "freebsd" ++#include ++#include ++#include ++#define bswap_16(x) bswap16(x) ++#define bswap_32(x) bswap32(x) ++#define bswap_64(x) bswap64(x) ++ ++#elif defined(__NetBSD__) ++ ++#define PROG_OS "netbsd" ++#include ++#include ++#include ++#define bswap_16(x) bswap16(x) ++#define bswap_32(x) bswap32(x) ++#define bswap_64(x) bswap64(x) ++// Alters behavior, but NetBSD 7 does not have getopt_long_only() ++#define getopt_long_only getopt_long ++ ++#else // Other Unix ++ ++#define PROG_OS "unknown" ++#include ++#include + #include + + #endif Property changes on: head/biology/vsearch/files/patch-src_vsearch.h ___________________________________________________________________ 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/vsearch/pkg-descr =================================================================== --- head/biology/vsearch/pkg-descr (nonexistent) +++ head/biology/vsearch/pkg-descr (revision 501147) @@ -0,0 +1,10 @@ +VSEARCH supports de novo and reference based chimera detection, clustering, +full-length and prefix dereplication, rereplication, reverse complementation, +masking, all-vs-all pairwise global alignment, exact and global alignment +searching, shuffling, subsampling and sorting. It also supports FASTQ file +analysis, filtering, conversion and merging of paired-end reads. + +The aim of this project is to create an alternative to the USEARCH tool +developed by Robert C. Edgar (2010). + +WWW: https://github.com/torognes/vsearch Property changes on: head/biology/vsearch/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