svn commit: r533993 - in head/biology: . plink plink/files
Jason W. Bacon
jwb at FreeBSD.org
Mon May 4 23:01:59 UTC 2020
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 at 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 at FreeBSD.org
+MAINTAINER= mzaki at 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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