ports/171922: New port: biology/plinkseq

[Jason Bacon]

>Number:         171922
>Category:       ports
>Synopsis:       New port: biology/plinkseq
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Sep 24 14:00:25 UTC 2012
>Closed-Date:
>Last-Modified:
>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 at 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 at 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 at 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:
>Unformatted: