CVS commit: pkgsrc/biology/vsearch

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/vsearch
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Fri, 10 May 2019 16:19:22 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri May 10 16:19:22 UTC 2019

Added Files:
        pkgsrc/biology/vsearch: DESCR Makefile PLIST distinfo
        pkgsrc/biology/vsearch/patches: patch-configure.ac
            patch-src_Makefile.am patch-src_city.cc patch-src_vsearch.h

Log Message:
biology/vsearch: import vsearch-2.13.3

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).


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/vsearch/DESCR \
    pkgsrc/biology/vsearch/Makefile pkgsrc/biology/vsearch/PLIST \
    pkgsrc/biology/vsearch/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/vsearch/patches/patch-configure.ac \
    pkgsrc/biology/vsearch/patches/patch-src_Makefile.am \
    pkgsrc/biology/vsearch/patches/patch-src_city.cc \
    pkgsrc/biology/vsearch/patches/patch-src_vsearch.h

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/vsearch/DESCR
diff -u /dev/null pkgsrc/biology/vsearch/DESCR:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/DESCR        Fri May 10 16:19:22 2019
@@ -0,0 +1,9 @@
+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).
Index: pkgsrc/biology/vsearch/Makefile
diff -u /dev/null pkgsrc/biology/vsearch/Makefile:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/Makefile     Fri May 10 16:19:22 2019
@@ -0,0 +1,26 @@
+# $NetBSD: Makefile,v 1.1 2019/05/10 16:19:22 bacon Exp $
+
+DISTNAME=      vsearch-2.13.3
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=torognes/}
+GITHUB_TAG=    v${PKGVERSION_NOREV}
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      https://github.com/torognes/vsearch
+COMMENT=       Versatile open-source tool for metagenomics
+LICENSE=       gnu-gpl-v3
+
+# Works on powerpc64, but only in little endian mode
+ONLY_FOR_PLATFORM=     *-*-aarch64 *-*-x86_64
+
+USE_LANGUAGES=         c c++
+USE_TOOLS+=            autoconf automake autoreconf gmake
+GNU_CONFIGURE=         yes
+CONFIGURE_ARGS+=       --disable-pdfman
+
+pre-configure:
+       cd ${WRKSRC} && autoreconf -fi
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/vsearch/PLIST
diff -u /dev/null pkgsrc/biology/vsearch/PLIST:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/PLIST        Fri May 10 16:19:22 2019
@@ -0,0 +1,3 @@
+@comment $NetBSD: PLIST,v 1.1 2019/05/10 16:19:22 bacon Exp $
+bin/vsearch
+man/man1/vsearch.1
Index: pkgsrc/biology/vsearch/distinfo
diff -u /dev/null pkgsrc/biology/vsearch/distinfo:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/distinfo     Fri May 10 16:19:22 2019
@@ -0,0 +1,10 @@
+$NetBSD: distinfo,v 1.1 2019/05/10 16:19:22 bacon Exp $
+
+SHA1 (vsearch-2.13.3.tar.gz) = 064bfbef4271c254848f18b03bed7c41a15ae2ab
+RMD160 (vsearch-2.13.3.tar.gz) = d8f00a88449fb827878b7e301f9127799ce3d43c
+SHA512 (vsearch-2.13.3.tar.gz) = a3c539d60ed6db8bdb964a1aee18e79a6b8ed397dc01d47aad873019a8f123ed8892b08536dfd5f785f8d327fee75d42b4a744f354f5c6e3bb03d0bf10f054e5
+Size (vsearch-2.13.3.tar.gz) = 233846 bytes
+SHA1 (patch-configure.ac) = 536a8565514cf9b43f4f8892d1cba0444f752c5e
+SHA1 (patch-src_Makefile.am) = bcdd1bbe9f04197084825e2c3560ba27a750f124
+SHA1 (patch-src_city.cc) = 3a5bcbca0a0c733a32a9d152189de10df3cb515f
+SHA1 (patch-src_vsearch.h) = 26b8dc6ce0448e7463ee1c3ff73747ad07286543

Index: pkgsrc/biology/vsearch/patches/patch-configure.ac
diff -u /dev/null pkgsrc/biology/vsearch/patches/patch-configure.ac:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/patches/patch-configure.ac   Fri May 10 16:19:22 2019
@@ -0,0 +1,16 @@
+$NetBSD: patch-configure.ac,v 1.1 2019/05/10 16:19:22 bacon Exp $
+
+# Respect build env
+
+--- 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
Index: pkgsrc/biology/vsearch/patches/patch-src_Makefile.am
diff -u /dev/null pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/patches/patch-src_Makefile.am        Fri May 10 16:19:22 2019
@@ -0,0 +1,22 @@
+$NetBSD: patch-src_Makefile.am,v 1.1 2019/05/10 16:19:22 bacon Exp $
+
+# Respect build env
+
+--- src/Makefile.am.orig       2019-04-30 11:57:32 UTC
++++ src/Makefile.am
+@@ -1,12 +1,12 @@
+ bin_PROGRAMS = $(top_builddir)/bin/vsearch
+ 
+ if TARGET_PPC
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+ if TARGET_AARCH64
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ endif
+ endif
+ 
Index: pkgsrc/biology/vsearch/patches/patch-src_city.cc
diff -u /dev/null pkgsrc/biology/vsearch/patches/patch-src_city.cc:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/patches/patch-src_city.cc    Fri May 10 16:19:22 2019
@@ -0,0 +1,20 @@
+$NetBSD: patch-src_city.cc,v 1.1 2019/05/10 16:19:22 bacon Exp $
+
+# 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>
Index: pkgsrc/biology/vsearch/patches/patch-src_vsearch.h
diff -u /dev/null pkgsrc/biology/vsearch/patches/patch-src_vsearch.h:1.1
--- /dev/null   Fri May 10 16:19:22 2019
+++ pkgsrc/biology/vsearch/patches/patch-src_vsearch.h  Fri May 10 16:19:22 2019
@@ -0,0 +1,67 @@
+$NetBSD: patch-src_vsearch.h,v 1.1 2019/05/10 16:19:22 bacon Exp $
+
+# Add FreeBSD and NetBSD support
+
+--- src/vsearch.h.orig 2019-04-30 11:57:32.000000000 +0000
++++ src/vsearch.h
+@@ -138,30 +138,50 @@
+ #define bswap_32(x) _byteswap_ulong(x)
+ #define bswap_64(x) _byteswap_uint64(x)
+ 
+-#else
+-
+-#ifdef __APPLE__
++#elif defined(__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 <machine/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

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