Date: Mon, 4 May 2020 23:01:58 +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: r533993 - in head/biology: . plink plink/files Message-ID: <202005042301.044N1wd2057310@repo.freebsd.org>
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Author: jwb Date: Mon May 4 23:01:57 2020 New Revision: 533993 URL: https://svnweb.freebsd.org/changeset/ports/533993 Log: biology/plink: Whole genome association analysis toolset Reversed removal, commit r471892 2018/06/07 Upgraded to 1.90 beta 6.17 PR: ports/243733 Submitted by: mzaki@e-mail.ne.jp Added: head/biology/plink/ - copied from r471891, head/biology/plink/ head/biology/plink/files/patch-plink__common.h (contents, props changed) head/biology/plink/pkg-plist (contents, props changed) Deleted: head/biology/plink/files/patch-Makefile head/biology/plink/files/patch-elf.cpp head/biology/plink/files/patch-idhelp.cpp head/biology/plink/files/patch-sets.cpp Modified: head/biology/Makefile head/biology/plink/Makefile head/biology/plink/distinfo head/biology/plink/pkg-descr Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon May 4 21:46:47 2020 (r533992) +++ head/biology/Makefile Mon May 4 23:01:57 2020 (r533993) @@ -114,6 +114,7 @@ SUBDIR += phred SUBDIR += phylip SUBDIR += phyml + SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal Modified: head/biology/plink/Makefile ============================================================================== --- head/biology/plink/Makefile Thu Jun 7 00:32:27 2018 (r471891) +++ head/biology/plink/Makefile Mon May 4 23:01:57 2020 (r533993) @@ -1,30 +1,57 @@ # $FreeBSD$ -PORTNAME= plink -PORTVERSION= 1.07 -PORTREVISION= 8 -CATEGORIES= biology science -MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ -DISTNAME= ${PORTNAME}-${PORTVERSION}-src +PORTNAME= plink +DISTVERSIONPREFIX= v +DISTVERSION= 1.90b6.17 +CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Whole genome association analysis toolset -BROKEN= no public distfiles -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2018-06-06 +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE -LICENSE= GPLv2 +NOT_FOR_ARCHS= aarch64 mips64 powerpc64 sparc64 +NOT_FOR_ARCHS_REASON= 64bit code requires SSE2 instructions -LIB_DEPENDS= liblapack.so:math/lapack +USES= gmake fortran -# We need Fortran LDFLAGS to link with Lapack. -USES= fortran gmake zip +USE_GITHUB= yes +GH_ACCOUNT= chrchang +GH_PROJECT= plink-ng +GH_TAGNAME= 79b2df8c -PLIST_FILES= bin/plink +WRKSRC_SUBDIR= 1.9 +MAKEFILE= Makefile.std +MAKE_ARGS= ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}" +CFLAGS+= -DDYNAMIC_ZLIB -I${LOCALBASE}/include +LDFLAGS+= -lthr +INSTALL_TARGET= install-strip -do-install: - ${MKDIR} ${STAGEDIR}${PREFIX}/bin - ${INSTALL_PROGRAM} ${WRKSRC}/plink ${STAGEDIR}${PREFIX}/bin +OPTIONS_DEFINE= EXAMPLES +OPTIONS_SINGLE= BLAS +OPTIONS_SINGLE_BLAS= NETLIB OPENBLAS +OPTIONS_DEFAULT= OPENBLAS + +BLAS_DESC= BLAS/LAPACK implementation + +OPENBLAS_USES= blaslapack:openblas + +NETLIB_DESC= Netlib's reference +NETLIB_USES= blaslapack:netlib +NETLIB_LIB_DEPENDS= libcblas.so:math/cblas +NETLIB_LDFLAGS= -lcblas + +EXAMPLES= toy.map toy.ped + +post-build: + (cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify) + +post-install: + ${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin + +post-install-EXAMPLES-on: + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR} .include <bsd.port.mk> Modified: head/biology/plink/distinfo ============================================================================== --- head/biology/plink/distinfo Thu Jun 7 00:32:27 2018 (r471891) +++ head/biology/plink/distinfo Mon May 4 23:01:57 2020 (r533993) @@ -1,2 +1,3 @@ -SHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b -SIZE (plink-1.07-src.zip) = 2257297 +TIMESTAMP = 1588630386 +SHA256 (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 1207dcabb4bf3f3f4ec5b0e4e5d66ec14075e2cd6d45dd318f13dfb8b4e57116 +SIZE (chrchang-plink-ng-v1.90b6.17-79b2df8c_GH0.tar.gz) = 3013121 Added: head/biology/plink/files/patch-plink__common.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/files/patch-plink__common.h Mon May 4 23:01:57 2020 (r533993) @@ -0,0 +1,20 @@ +--- plink_common.h.orig 2020-01-22 01:51:56 UTC ++++ plink_common.h +@@ -122,7 +122,7 @@ + #define EOLN_STR "\n" + #define FOPEN_RB "r" + #define FOPEN_WB "w" +- #ifndef __APPLE__ ++ #if !defined(__APPLE__) && !defined(__FreeBSD__) + // argh + // not sure what the right threshold actually is, but this works for now + // (may break on gcc <3.0? but that shouldn't matter anymore) +@@ -143,7 +143,7 @@ + #define CLZLU __builtin_clzl + #ifndef __LP64__ + // attempt to patch GCC 6 build failure +- #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) ++ #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) + #ifndef uintptr_t + #define uintptr_t unsigned long + #endif Modified: head/biology/plink/pkg-descr ============================================================================== --- head/biology/plink/pkg-descr Thu Jun 7 00:32:27 2018 (r471891) +++ head/biology/plink/pkg-descr Mon May 4 23:01:57 2020 (r533993) @@ -1,5 +1,9 @@ -PLINK is a free, open-source whole genome association analysis toolset, -designed to perform a range of basic, large-scale analyses in a -computationally efficient manner. +PLINK is a widely used toolset for genome-wide association studies (GWAS) and +research in population genetics. -WWW: http://pngu.mgh.harvard.edu/~purcell/plink/ +Citation: +Chang et al. (2015) +Second-generation PLINK: rising to the challenge of larger and richer datasets. +GigaScience 4(1) doi:10.1186/s13742-015-0047-8 + +WWW: https://www.cog-genomics.org/plink/ Added: head/biology/plink/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/pkg-plist Mon May 4 23:01:57 2020 (r533993) @@ -0,0 +1,4 @@ +bin/plink +bin/prettify +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped
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