Attachment 211196 Details for Bug 243733 – shar for biology/plink version 1.90b6.15

shar for biology/plink version 1.90b6.15

plink.shar (text/plain), 3.78 KB, created by Motomichi Matsuzaki on 2020-01-30 16:29:04 UTC

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Creator: Motomichi Matsuzaki

Created: 2020-01-30 16:29:04 UTC

Size: 3.78 KB

patch

obsolete

># This is a shell archive.  Save it in a file, remove anything before
># this line, and then unpack it by entering "sh file".  Note, it may
># create directories; files and directories will be owned by you and
># have default permissions.
>#
># This archive contains:
>#
>#	plink
>#	plink/pkg-descr
>#	plink/files
>#	plink/files/patch-plink__common.h
>#	plink/Makefile
>#	plink/pkg-plist
>#	plink/distinfo
>#
>echo c - plink
>mkdir -p plink > /dev/null 2>&1
>echo x - plink/pkg-descr
>sed 's/^X//' >plink/pkg-descr << '13db0b698fc1987e35a2140396ca451a'
>XPLINK is a widely used toolset for genome-wide association studies (GWAS) and
>Xresearch in population genetics.
>X
>XCitation:
>XChang et al. (2015)
>XSecond-generation PLINK: rising to the challenge of larger and richer datasets.
>XGigaScience 4(1) doi:10.1186/s13742-015-0047-8
>X
>XWWW: https://www.cog-genomics.org/plink/
>13db0b698fc1987e35a2140396ca451a
>echo c - plink/files
>mkdir -p plink/files > /dev/null 2>&1
>echo x - plink/files/patch-plink__common.h
>sed 's/^X//' >plink/files/patch-plink__common.h << 'd9ed87deb2e2c367366dde611e36b2ec'
>X--- plink_common.h.orig	2020-01-22 01:51:56 UTC
>X+++ plink_common.h
>X@@ -122,7 +122,7 @@
>X   #define EOLN_STR "\n"
>X   #define FOPEN_RB "r"
>X   #define FOPEN_WB "w"
>X-  #ifndef __APPLE__
>X+  #if !defined(__APPLE__) && !defined(__FreeBSD__)
>X     // argh
>X     // not sure what the right threshold actually is, but this works for now
>X     // (may break on gcc <3.0?  but that shouldn't matter anymore)
>X@@ -143,7 +143,7 @@
>X   #define CLZLU __builtin_clzl
>X   #ifndef __LP64__
>X     // attempt to patch GCC 6 build failure
>X-    #if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
>X+    #if !defined(__FreeBSD__) && (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
>X       #ifndef uintptr_t
>X         #define uintptr_t unsigned long
>X       #endif
>d9ed87deb2e2c367366dde611e36b2ec
>echo x - plink/Makefile
>sed 's/^X//' >plink/Makefile << '3225f885242ffc903c9410142479cfcd'
>X# $FreeBSD$
>X
>XPORTNAME=	plink
>XDISTVERSIONPREFIX=	v
>XDISTVERSION=	1.90b6.15
>XCATEGORIES=	biology
>X
>XMAINTAINER=	mzaki@e-mail.ne.jp
>XCOMMENT=	Whole genome association analysis toolset
>X
>XLICENSE=	GPLv3
>XLICENSE_FILE=	${WRKSRC}/LICENSE
>X
>XNOT_FOR_ARCHS=	aarch64 mips64 powerpc64 sparc64
>XNOT_FOR_ARCHS_REASON=	64bit code requires SSE2 instructions
>X
>XUSES=		gmake fortran
>X
>XUSE_GITHUB=	yes
>XGH_ACCOUNT=	chrchang
>XGH_PROJECT=	plink-ng
>XGH_TAGNAME=	ebf119
>X
>XWRKSRC_SUBDIR=	1.9
>XMAKEFILE=	Makefile.std
>XMAKE_ARGS=	ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}"
>XCFLAGS+=	-DDYNAMIC_ZLIB -I${LOCALBASE}/include
>XLDFLAGS+=	-lthr
>XINSTALL_TARGET=	install-strip
>X
>XOPTIONS_DEFINE=		EXAMPLES
>XOPTIONS_SINGLE=		BLAS
>XOPTIONS_SINGLE_BLAS=	NETLIB OPENBLAS
>XOPTIONS_DEFAULT=	OPENBLAS
>X
>XBLAS_DESC=	BLAS/LAPACK implementation
>X
>XOPENBLAS_USES=	blaslapack:openblas
>X
>XNETLIB_DESC=	Netlib's reference
>XNETLIB_USES=	blaslapack:netlib
>XNETLIB_LIB_DEPENDS=	libcblas.so:math/cblas
>XNETLIB_LDFLAGS=	-lcblas
>X
>XEXAMPLES=	toy.map toy.ped
>X
>Xpost-build:
>X	(cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify)
>X
>Xpost-install:
>X	${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin
>X
>Xpost-install-EXAMPLES-on:
>X	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
>X	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR}
>X
>X.include <bsd.port.mk>
>3225f885242ffc903c9410142479cfcd
>echo x - plink/pkg-plist
>sed 's/^X//' >plink/pkg-plist << '03e964e537cb83fc44658a36a53a638a'
>Xbin/plink
>Xbin/prettify
>X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.map
>X%%PORTEXAMPLES%%%%EXAMPLESDIR%%/toy.ped
>03e964e537cb83fc44658a36a53a638a
>echo x - plink/distinfo
>sed 's/^X//' >plink/distinfo << 'a7e532cb61dd2baca4095cee307ed431'
>XTIMESTAMP = 1580352274
>XSHA256 (chrchang-plink-ng-v1.90b6.15-ebf119_GH0.tar.gz) = 130fc787be200a2b94eccc945e0844e00b9433fc87314c86ef95f3c0160fc012
>XSIZE (chrchang-plink-ng-v1.90b6.15-ebf119_GH0.tar.gz) = 2932982
>a7e532cb61dd2baca4095cee307ed431
>exit
>

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