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Date: Mon, 24 Sep 2012 13:53:49 GMT
From: Jason Bacon <jwbacon@tds.net>
To: freebsd-gnats-submit@FreeBSD.org
Subject: New port: biology/plinkseq
X-Send-Pr-Version: www-3.1
X-GNATS-Notify:

>Number:         171922
>Category:       ports
>Synopsis:       New port: biology/plinkseq
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    makc
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Sep 24 14:00:25 UTC 2012
>Closed-Date:    Thu Sep 27 10:00:26 UTC 2012
>Last-Modified:  Thu Sep 27 10:10:04 UTC 2012
>Originator:     Jason Bacon
>Release:        9.0-RELEASE
>Organization:
Acadix Consulting, LLC
>Environment:
FreeBSD sculpin.jbacon.dyndns.org 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan  3 07:46:30 UTC 2012     root@farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  amd64

>Description:
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.

>How-To-Repeat:

>Fix:


Patch attached with submission follows:

# 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:
#
#	plinkseq
#	plinkseq/pkg-descr
#	plinkseq/Makefile
#	plinkseq/pkg-plist
#	plinkseq/distinfo
#
echo c - plinkseq
mkdir -p plinkseq > /dev/null 2>&1
echo x - plinkseq/pkg-descr
sed 's/^X//' >plinkseq/pkg-descr << 'bacf232f9cecbb3e3b9b866dd40bb1cf'
XPLINK/SEQ is an open-source C/C++ library for working with human genetic
Xvariation data. The specific focus is to provide a platform for analytic tool
Xdevelopment for variation data from large-scale resequencing and genotyping
Xprojects, particularly whole-exome and whole-genome studies. It is independent
Xof (but designed to be complementary to) the existing PLINK package.
X
XWWW:	http://atgu.mgh.harvard.edu/plinkseq/
bacf232f9cecbb3e3b9b866dd40bb1cf
echo x - plinkseq/Makefile
sed 's/^X//' >plinkseq/Makefile << '01f8db9920f39f93248e063672899cd8'
X# New ports collection makefile for:	plinkseq
X# Date created:		06 September 2012
X# Whom:			Jason Bacon <jwbacon@tds.net>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	plinkseq
XPORTVERSION=	0.08
XCATEGORIES=	biology science
XMASTER_SITES=	http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/
X
XMAINTAINER=	jwbacon@tds.net
XCOMMENT=	A toolset for working with human genetic variation data
X
XLICENSE=	GPLv2
X
XLIB_DEPENDS=	protobuf:${PORTSDIR}/devel/protobuf
X
XUSE_DOS2UNIX=	yes
XUSE_LDCONFIG=	yes
XGNU_CONFIGURE=	yes
XCONFIGURE_ARGS+=--with-protobuf=${LOCALBASE}
X
Xpost-patch:
X	${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c
X	${REINPLACE_CMD} -e 's|-ldl||g' \
X		${WRKSRC}/browser/Makefile.in \
X		${WRKSRC}/client/Makefile.in \
X		${WRKSRC}/index/Makefile.in
X
X.include <bsd.port.mk>
01f8db9920f39f93248e063672899cd8
echo x - plinkseq/pkg-plist
sed 's/^X//' >plinkseq/pkg-plist << '34f02599c75e4950ca1bd20735d356cb'
Xbin/behead
Xbin/gcol
Xbin/index
Xbin/index.cgi
Xbin/mongoose
Xbin/pbrowse
Xbin/pbrowse.cgi
Xbin/pseq
Xbin/tab2vcf
Xlib/libplinkseq.la
Xlib/libplinkseq.so
Xlib/libplinkseq.so.0
34f02599c75e4950ca1bd20735d356cb
echo x - plinkseq/distinfo
sed 's/^X//' >plinkseq/distinfo << '85239e4941d225b70ec996841d9daa0e'
XSHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f
XSIZE (plinkseq-0.08.tar.gz) = 2991871
85239e4941d225b70ec996841d9daa0e
exit



>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->makc 
Responsible-Changed-By: makc 
Responsible-Changed-When: Tue Sep 25 14:10:22 UTC 2012 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=171922 
State-Changed-From-To: open->closed 
State-Changed-By: makc 
State-Changed-When: Thu Sep 27 10:00:22 UTC 2012 
State-Changed-Why:  
New port added. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=171922 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/171922: commit references a PR
Date: Thu, 27 Sep 2012 09:59:41 +0000 (UTC)

 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 <jwbacon at tds.net>
 
 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 <jwbacon@tds.net>
 +# $FreeBSD$
 +
 +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 <bsd.port.mk>
 
 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 <jwbacon@tds.net>
 +# $FreeBSD$
 +
 +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 <bsd.port.mk>
 
 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
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>Unformatted:
