From owner-svn-ports-head@FreeBSD.ORG Thu Sep 27 09:59:26 2012 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 0A444106566B; Thu, 27 Sep 2012 09:59:26 +0000 (UTC) (envelope-from makc@FreeBSD.org) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:4f8:fff6::2c]) by mx1.freebsd.org (Postfix) with ESMTP id E43558FC16; Thu, 27 Sep 2012 09:59:25 +0000 (UTC) Received: from svn.freebsd.org (localhost [127.0.0.1]) by svn.freebsd.org (8.14.4/8.14.4) with ESMTP id q8R9xPg1094120; Thu, 27 Sep 2012 09:59:25 GMT (envelope-from makc@svn.freebsd.org) Received: (from makc@localhost) by svn.freebsd.org (8.14.4/8.14.4/Submit) id q8R9xPG7094111; Thu, 27 Sep 2012 09:59:25 GMT (envelope-from makc@svn.freebsd.org) Message-Id: <201209270959.q8R9xPG7094111@svn.freebsd.org> From: Max Brazhnikov Date: Thu, 27 Sep 2012 09:59:25 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Cc: Subject: svn commit: r304954 - in head/biology: . plink plink/files plinkseq X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 27 Sep 2012 09:59:26 -0000 Author: makc Date: Thu Sep 27 09:59:25 2012 New Revision: 304954 URL: http://svn.freebsd.org/changeset/ports/304954 Log: Add new ports biology/plink [1] and biology/plinkseq [2]: PLINK is a free, open-source whole genome association analysis toolset. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. PR: ports/171918 [1] PR: ports/171922 [2] Submitted by: Jason Bacon Added: head/biology/plink/ head/biology/plink/Makefile (contents, props changed) head/biology/plink/distinfo (contents, props changed) head/biology/plink/files/ head/biology/plink/files/patch-Makefile (contents, props changed) head/biology/plink/pkg-descr (contents, props changed) head/biology/plinkseq/ head/biology/plinkseq/Makefile (contents, props changed) head/biology/plinkseq/distinfo (contents, props changed) head/biology/plinkseq/pkg-descr (contents, props changed) head/biology/plinkseq/pkg-plist (contents, props changed) Modified: head/biology/Makefile (contents, props changed) Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Sep 27 09:45:38 2012 (r304953) +++ head/biology/Makefile Thu Sep 27 09:59:25 2012 (r304954) @@ -72,6 +72,8 @@ SUBDIR += phylip SUBDIR += phyml SUBDIR += platon + SUBDIR += plink + SUBDIR += plinkseq SUBDIR += povchem SUBDIR += primer3 SUBDIR += protomol Added: head/biology/plink/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/Makefile Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,27 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= plink +PORTVERSION= 1.07 +CATEGORIES= biology science +MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ +DISTNAME= ${PORTNAME}-${PORTVERSION}-src + +MAINTAINER= jwbacon@tds.net +COMMENT= Whole genome association analysis toolset + +LICENSE= GPLv2 + +LIB_DEPENDS= lapack:${PORTSDIR}/math/lapack + +USE_ZIP= yes +USE_GMAKE= yes +USE_FORTRAN= yes # Make it use the same compiler as lapack + +PLIST_FILES= bin/plink + +do-install: + ${MKDIR} ${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin + +.include Added: head/biology/plink/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/distinfo Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,2 @@ +SHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b +SIZE (plink-1.07-src.zip) = 2257297 Added: head/biology/plink/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/files/patch-Makefile Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,52 @@ +--- Makefile.orig 2009-10-10 11:00:20.000000000 -0500 ++++ Makefile 2012-09-07 08:24:26.000000000 -0500 +@@ -26,7 +26,7 @@ + WITH_WEBCHECK = 1 + FORCE_32BIT = + WITH_ZLIB = 1 +-WITH_LAPACK = ++WITH_LAPACK = 1 + FORCE_DYNAMIC = + + # Put C++ compiler here; Windows has it's own specific version +@@ -34,17 +34,17 @@ + CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe + + # Any other compiler flags here ( -Wall, -g, etc) +-CXXFLAGS = ++# CXXFLAGS = + + # Misc +-LIB_LAPACK = /usr/lib/liblapack.so.3 ++LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran + + + # -------------------------------------------------------------------- + # Do not edit below this line + # -------------------------------------------------------------------- + +-CXXFLAGS += -O3 -I. ++CXXFLAGS += -I. + OUTPUT = plink + + # Some system specific flags +@@ -58,8 +58,8 @@ + endif + + ifeq ($(SYS),UNIX) +- CXXFLAGS += -DUNIX +- CXX = $(CXX_UNIX) ++ CXXFLAGS += -DUNIX -Dfopen64=fopen ++ CXX ?= $(CXX_UNIX) + ifndef FORCE_DYNAMIC + CXXFLAGS += -static + endif +@@ -128,7 +128,7 @@ + LIB += -ldl + endif + ifeq ($(SYS),UNIX) +-LIB += -ldl -lcrypt ++LIB += -lcrypt + endif + endif + Added: head/biology/plink/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plink/pkg-descr Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,5 @@ +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. + +WWW: http://pngu.mgh.harvard.edu/~purcell/plink/ Added: head/biology/plinkseq/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plinkseq/Makefile Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,28 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= plinkseq +PORTVERSION= 0.08 +CATEGORIES= biology science +MASTER_SITES= http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/ + +MAINTAINER= jwbacon@tds.net +COMMENT= Toolset for working with human genetic variation data + +LICENSE= GPLv2 + +LIB_DEPENDS= protobuf:${PORTSDIR}/devel/protobuf + +USE_DOS2UNIX= yes +USE_LDCONFIG= yes +GNU_CONFIGURE= yes +CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE} + +post-patch: + ${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c + ${REINPLACE_CMD} -e 's|-ldl||g' \ + ${WRKSRC}/browser/Makefile.in \ + ${WRKSRC}/client/Makefile.in \ + ${WRKSRC}/index/Makefile.in + +.include Added: head/biology/plinkseq/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plinkseq/distinfo Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,2 @@ +SHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f +SIZE (plinkseq-0.08.tar.gz) = 2991871 Added: head/biology/plinkseq/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plinkseq/pkg-descr Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,8 @@ +PLINK/SEQ is an open-source C/C++ library for working with human +genetic variation data. The specific focus is to provide a platform +for analytic tool development for variation data from large-scale +resequencing and genotyping projects, particularly whole-exome and +whole-genome studies. It is independent of (but designed to be +complementary to) the existing PLINK package. + +WWW: http://atgu.mgh.harvard.edu/plinkseq/ Added: head/biology/plinkseq/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/plinkseq/pkg-plist Thu Sep 27 09:59:25 2012 (r304954) @@ -0,0 +1,12 @@ +bin/behead +bin/gcol +bin/index +bin/index.cgi +bin/mongoose +bin/pbrowse +bin/pbrowse.cgi +bin/pseq +bin/tab2vcf +lib/libplinkseq.la +lib/libplinkseq.so +lib/libplinkseq.so.0