Date: Thu, 9 May 2019 21:28:49 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r501147 - in head/biology: . vsearch vsearch/files Message-ID: <201905092128.x49LSnx6078466@repo.freebsd.org>
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Author: jwb Date: Thu May 9 21:28:49 2019 New Revision: 501147 URL: https://svnweb.freebsd.org/changeset/ports/501147 Log: biology/vsearch: Versatile open-source tool for metagenomics 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). Added: head/biology/vsearch/ head/biology/vsearch/Makefile (contents, props changed) head/biology/vsearch/distinfo (contents, props changed) head/biology/vsearch/files/ head/biology/vsearch/files/patch-configure.ac (contents, props changed) head/biology/vsearch/files/patch-src_Makefile.am (contents, props changed) head/biology/vsearch/files/patch-src_city.cc (contents, props changed) head/biology/vsearch/files/patch-src_vsearch.h (contents, props changed) head/biology/vsearch/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu May 9 20:12:51 2019 (r501146) +++ head/biology/Makefile Thu May 9 21:28:49 2019 (r501147) @@ -158,6 +158,7 @@ SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet + SUBDIR += vsearch SUBDIR += wise .include <bsd.port.subdir.mk> Added: head/biology/vsearch/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/Makefile Thu May 9 21:28:49 2019 (r501147) @@ -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 <bsd.port.mk> Added: head/biology/vsearch/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/distinfo Thu May 9 21:28:49 2019 (r501147) @@ -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 Added: head/biology/vsearch/files/patch-configure.ac ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/files/patch-configure.ac Thu May 9 21:28:49 2019 (r501147) @@ -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 Added: head/biology/vsearch/files/patch-src_Makefile.am ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/files/patch-src_Makefile.am Thu May 9 21:28:49 2019 (r501147) @@ -0,0 +1,18 @@ +--- src/Makefile.am.orig 2019-04-30 11:57:32 UTC ++++ src/Makefile.am +@@ -1,12 +1,12 @@ + bin_PROGRAMS = $(top_builddir)/bin/vsearch + + if TARGET_PPC +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8 ++AM_CXXFLAGS=-Wall -Wsign-compare + else + if TARGET_AARCH64 +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic ++AM_CXXFLAGS=-Wall -Wsign-compare + else +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic ++AM_CXXFLAGS=-Wall -Wsign-compare + endif + endif + Added: head/biology/vsearch/files/patch-src_city.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/files/patch-src_city.cc Thu May 9 21:28:49 2019 (r501147) @@ -0,0 +1,20 @@ +$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 <sys/endian.h> ++ ++#define bswap_32(x) bswap32(x) ++#define bswap_64(x) bswap64(x) ++ + #elif defined(__NetBSD__) + + #include <sys/types.h> Added: head/biology/vsearch/files/patch-src_vsearch.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/files/patch-src_vsearch.h Thu May 9 21:28:49 2019 (r501147) @@ -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 <sys/sysctl.h> + #include <libkern/OSByteOrder.h> ++#include <sys/resource.h> + #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 <sys/sysinfo.h> + #include <byteswap.h> ++#include <sys/resource.h> + +-#endif ++#elif defined(__FreeBSD__) + ++#define PROG_OS "freebsd" ++#include <sys/sysinfo.h> ++#include <sys/resource.h> ++#include <sys/endian.h> ++#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 <sys/resource.h> ++#include <sys/types.h> ++#include <sys/bswap.h> ++#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 <sys/sysinfo.h> ++#include <byteswap.h> + #include <sys/resource.h> + + #endif Added: head/biology/vsearch/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vsearch/pkg-descr Thu May 9 21:28:49 2019 (r501147) @@ -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
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