diff options
author | bacon <bacon@pkgsrc.org> | 2019-05-10 16:19:22 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2019-05-10 16:19:22 +0000 |
commit | fcf2e1323db6e24309f34808d2e977477e8a8d8e (patch) | |
tree | 4a79ebc8123cfffe20fe51819ddf8ff2f778a889 /biology | |
parent | 02b3bfbc515f986411e1753afdabee17e4b96137 (diff) | |
download | pkgsrc-fcf2e1323db6e24309f34808d2e977477e8a8d8e.tar.gz |
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).
Diffstat (limited to 'biology')
-rw-r--r-- | biology/vsearch/DESCR | 9 | ||||
-rw-r--r-- | biology/vsearch/Makefile | 26 | ||||
-rw-r--r-- | biology/vsearch/PLIST | 3 | ||||
-rw-r--r-- | biology/vsearch/distinfo | 10 | ||||
-rw-r--r-- | biology/vsearch/patches/patch-configure.ac | 16 | ||||
-rw-r--r-- | biology/vsearch/patches/patch-src_Makefile.am | 22 | ||||
-rw-r--r-- | biology/vsearch/patches/patch-src_city.cc | 20 | ||||
-rw-r--r-- | biology/vsearch/patches/patch-src_vsearch.h | 67 |
8 files changed, 173 insertions, 0 deletions
diff --git a/biology/vsearch/DESCR b/biology/vsearch/DESCR new file mode 100644 index 00000000000..e862cf83eb7 --- /dev/null +++ b/biology/vsearch/DESCR @@ -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). diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile new file mode 100644 index 00000000000..6ecf6920f73 --- /dev/null +++ b/biology/vsearch/Makefile @@ -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 +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" diff --git a/biology/vsearch/PLIST b/biology/vsearch/PLIST new file mode 100644 index 00000000000..2d78ae1c55d --- /dev/null +++ b/biology/vsearch/PLIST @@ -0,0 +1,3 @@ +@comment $NetBSD: PLIST,v 1.1 2019/05/10 16:19:22 bacon Exp $ +bin/vsearch +man/man1/vsearch.1 diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo new file mode 100644 index 00000000000..dbc5a9d3d9a --- /dev/null +++ b/biology/vsearch/distinfo @@ -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 diff --git a/biology/vsearch/patches/patch-configure.ac b/biology/vsearch/patches/patch-configure.ac new file mode 100644 index 00000000000..c4176c10f26 --- /dev/null +++ b/biology/vsearch/patches/patch-configure.ac @@ -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 diff --git a/biology/vsearch/patches/patch-src_Makefile.am b/biology/vsearch/patches/patch-src_Makefile.am new file mode 100644 index 00000000000..8e00fefdaf3 --- /dev/null +++ b/biology/vsearch/patches/patch-src_Makefile.am @@ -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 = $(top_builddir)/bin/vsearch + + if TARGET_PPC +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8 ++AM_CXXFLAGS=-Wall -Wsign-compare + else + if TARGET_AARCH64 +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic ++AM_CXXFLAGS=-Wall -Wsign-compare + else +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic ++AM_CXXFLAGS=-Wall -Wsign-compare + endif + endif + diff --git a/biology/vsearch/patches/patch-src_city.cc b/biology/vsearch/patches/patch-src_city.cc new file mode 100644 index 00000000000..77346020c82 --- /dev/null +++ b/biology/vsearch/patches/patch-src_city.cc @@ -0,0 +1,20 @@ +$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> diff --git a/biology/vsearch/patches/patch-src_vsearch.h b/biology/vsearch/patches/patch-src_vsearch.h new file mode 100644 index 00000000000..7c4343180b2 --- /dev/null +++ b/biology/vsearch/patches/patch-src_vsearch.h @@ -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 |