Date: Mon, 24 Sep 2012 13:53:49 GMT From: Jason Bacon <jwbacon@tds.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/171922: New port: biology/plinkseq Message-ID: <201209241353.q8ODrnTx077411@red.freebsd.org> Resent-Message-ID: <201209241400.q8OE0QC8048846@freefall.freebsd.org>
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>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@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: >Unformatted:
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