ports/120129: New port: science/dtiquery DTI Visualization Software

Jason Bacon bacon at smithers.neuro.mcw.edu
Tue Jan 29 21:50:02 UTC 2008 

>Number:         120129
>Category:       ports
>Synopsis:       New port: science/dtiquery  DTI Visualization Software
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Tue Jan 29 21:50:01 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Jason Bacon
>Release:        FreeBSD 6.1-RELEASE-p17 i386
>Organization:
MCW
>Environment:
System: FreeBSD smithers.neuro.mcw.edu 6.1-RELEASE-p17 FreeBSD 6.1-RELEASE-p17 #0: Mon Jul 2 15:25:34 CDT 2007 bacon at pcbsd:/usr/obj/usr/src/sys/MCWPCBSD i386

>Description:

DTIQuery is a software package for visualizing Diffusion Tensor Imaging data.

>How-To-Repeat:
>Fix:

# 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:
#
#	science/dtiquery
#	science/dtiquery/files
#	science/dtiquery/files/dtiquery.1
#	science/dtiquery/files/pkg-message.in
#	science/dtiquery/files/patch-DTIQuery-Makefile
#	science/dtiquery/files/patch-Makefile.definitions
#	science/dtiquery/files/patch-precompute-Makefile
#	science/dtiquery/Makefile
#	science/dtiquery/distinfo
#	science/dtiquery/pkg-descr
#
echo c - science/dtiquery
mkdir -p science/dtiquery > /dev/null 2>&1
echo c - science/dtiquery/files
mkdir -p science/dtiquery/files > /dev/null 2>&1
echo x - science/dtiquery/files/dtiquery.1
sed 's/^X//' >science/dtiquery/files/dtiquery.1 << 'END-of-science/dtiquery/files/dtiquery.1'
X.TH DTIQUERY 1
X.SH NAME    \" Section header
X.PP
X
XDTIQuery - DTI Visualization Software
X
X.SH SYNOPSIS
X.PP
X.nf 
X.na 
Xdtiquery
Xdtiprecompute_cmd [args]
Xdtiprecompute_gui
X
X.ad
X.fi
X
X.SH "DESCRIPTION"
X
XDTIQuery is a software suite for analyzing DTI (Diffusion Tensor Imaging)
Xdata obtained via MRI (Magnetic Resonence Imaging).  For full documentation,
Xplease visit 
X
Xhttp://graphics.stanford.edu/projects/dti/software/.
X
X.SH "SEE ALSO"
X
Xafni(1), caret(1), freesurfer(1), fsl(1)
X
X.SH AUTHOR
X.nf
X.na
XDavid Akers
XStanford University
X
END-of-science/dtiquery/files/dtiquery.1
echo x - science/dtiquery/files/pkg-message.in
sed 's/^X//' >science/dtiquery/files/pkg-message.in << 'END-of-science/dtiquery/files/pkg-message.in'
X=============================================================================
XDTI Query users will need %%PREFIX%%/bin in their PATH.
X
XFor questions or comments regarding this port, please contact the
Xport maintainer.
X
XFor dtiquery usage, please visit the WEB site at
X
Xhttp://graphics.stanford.edu/projects/dti/
X=============================================================================
END-of-science/dtiquery/files/pkg-message.in
echo x - science/dtiquery/files/patch-DTIQuery-Makefile
sed 's/^X//' >science/dtiquery/files/patch-DTIQuery-Makefile << 'END-of-science/dtiquery/files/patch-DTIQuery-Makefile'
X--- DTIQuery/Makefile.orig	Thu Dec  6 13:48:54 2007
X+++ DTIQuery/Makefile	Thu Dec  6 13:49:24 2007
X@@ -12,8 +12,8 @@
X 
X VTK_LIBS = -lvtkIO \
X         -lvtkRendering -lvtkGraphics -lvtkImaging \
X-        -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \
X-        -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \
X+        -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \
X+        -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \
X 
X # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg
X 
END-of-science/dtiquery/files/patch-DTIQuery-Makefile
echo x - science/dtiquery/files/patch-Makefile.definitions
sed 's/^X//' >science/dtiquery/files/patch-Makefile.definitions << 'END-of-science/dtiquery/files/patch-Makefile.definitions'
X--- Makefile.definitions.orig	Wed Dec 19 10:50:50 2007
X+++ Makefile.definitions	Wed Dec 19 10:51:13 2007
X@@ -1,6 +1,6 @@
X-CYGWIN = 1
X+# CYGWIN = 1
X # mac = 1
X-# FreeBSD = 1
X+FreeBSD = 1
X # linux = 1
X 
X # Uncomment the line above corresponding to your system. Then find the 
X@@ -46,18 +46,19 @@
X 
X ifdef FreeBSD
X 
X-WX_CONFIG_BIN		?= /usr/X11R6/bin/wxgtk2-2.8-config
X+WX_CONFIG_BIN		?= ${X11BASE}/bin/wxgtk2-2.8-config
X VTK_INCLUDE_PATHS	?= -I/usr/local/include/vtk-5.0/
X VTK_LIB_PATHS		?= -L/usr/local/lib/vtk-5.0/
X WX_INCLUDE_PATHS	?= `$(WX_CONFIG_BIN) --cxxflags`
X WX_LIB_PATHS		?= `$(WX_CONFIG_BIN) --libs` `$(WX_CONFIG_BIN) \
X 				--gl-libs`
X-RAPID_INCLUDE_PATH	?= -I/usr/local/include
X+RAPID_INCLUDE_PATH	?= -I/usr/local/include/RAPID
X RAPID_LIB_PATH		?= -L/usr/local/lib
X TNT_INCLUDE_PATH	?= -I/usr/local/include/tnt/
X JAMA_INCLUDE_PATH	?= -I/usr/local/include/
X ZLIB_INCLUDE_PATH	?= -I/usr/include
X-SYS_INCLUDE_PATHS	?= -I/usr/include -I/usr/X11R6/include -I/usr/local/include/gtk-2.0 -I/usr/X11R6/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I/usr/X11R6/include/pango-1.0 -I/usr/local/include/atk-1.0 
X+SYS_INCLUDE_PATHS	?= -I/usr/include -I${X11BASE}/include -I/usr/local/include/gtk-2.0 -I${X11BASE}/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I${X11BASE}/include/pango-1.0 -I/usr/local/include/atk-1.0 
X+SYS_CXXFLAGS 		?= -g
X SYS_LIBS		?= -L/usr/local/lib -lXt -lGL -lpng
X 
X else
END-of-science/dtiquery/files/patch-Makefile.definitions
echo x - science/dtiquery/files/patch-precompute-Makefile
sed 's/^X//' >science/dtiquery/files/patch-precompute-Makefile << 'END-of-science/dtiquery/files/patch-precompute-Makefile'
X--- precompute/Makefile.orig	Thu Dec  6 13:51:44 2007
X+++ precompute/Makefile	Thu Dec  6 13:52:16 2007
X@@ -21,8 +21,8 @@
X 
X VTK_LIBS = -lvtkIO \
X         -lvtkRendering -lvtkGraphics -lvtkImaging \
X-        -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \
X-        -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \
X+        -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \
X+        -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \
X 
X # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg
X 
END-of-science/dtiquery/files/patch-precompute-Makefile
echo x - science/dtiquery/Makefile
sed 's/^X//' >science/dtiquery/Makefile << 'END-of-science/dtiquery/Makefile'
X############################################################################
X# New ports collection Makefile for:   DTI-Query
X# Date created:        10 July 2006
X# Whom:                Jason W. Bacon <jwbacon at tds.net>
X#
X# $FreeBSD$
X#
X############################################################################
X
XPORTNAME=	dtiquery
XPORTVERSION=	1.1
XCATEGORIES=	science biology
XMASTER_SITES=	http://graphics.stanford.edu/projects/dti/
X
XMAINTAINER=	jwbacon at tds.net
XCOMMENT=	Stanford DTI Visualization tool
X
XBUILD_DEPENDS=	${LOCALBASE}/include/tnt/tnt.h:${PORTSDIR}/devel/tnt \
X		${LOCALBASE}/include/tnt/jama_cholesky.h:${PORTSDIR}/math/jama \
X		${LOCALBASE}/lib/libRAPID.a:${PORTSDIR}/math/rapid
XEXTRACT_DEPENDS=	dos2unix:${PORTSDIR}/converters/unix2dos
XLIB_DEPENDS=	wx_gtk2_core-2.8.0:${PORTSDIR}/x11-toolkits/wxgtk28 \
X		vtkCommon.5:${PORTSDIR}/math/vtk5
X
XCONFLICTS=	dtiquery-1.0*
X
XRESTRICTED=	Must register to download at http://graphics.stanford.edu/projects/dti/
X
XSUB_FILES=	pkg-message
XPKGMESSAGE=	${WRKDIR}/pkg-message
X
XUSE_GMAKE=	yes
X
XPLIST_FILES=	bin/dtiquery \
X		bin/dtiprecompute_cmd \
X		bin/dtiprecompute_gui
X
XALL_TARGET=
X
XMAN1=		dtiquery.1 \
X		dtiprecompute_cmd.1 \
X		dtiprecompute_gui.1
X
X.include <bsd.port.pre.mk>
X
X.if !exists(${DISTDIR}/${DISTNAME}.tar.gz)
XIGNORE=	you must manually fetch ${DISTNAME}.tar.gz from http://graphics.stanford.edu/projects/dti/, place it in ${DISTDIR}, and then run make again
X.endif
X
Xpost-extract:
X	dos2unix ${WRKSRC}/*/Makefile ${WRKSRC}/Makefile*
X	${REINPLACE_CMD} "s/zlib-1.2.2 RAPID201//g" ${WRKSRC}/Makefile
X
Xdo-install:
X	${INSTALL_PROGRAM} ${WRKSRC}/DTIQuery/dtiquery ${PREFIX}/bin
X	${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_cmd ${PREFIX}/bin
X	${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_gui ${PREFIX}/bin
X	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1
X	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_cmd.1
X	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_gui.1
X
Xpost-install:
X	@${CAT} ${PKGMESSAGE}
X
X.include <bsd.port.post.mk>
END-of-science/dtiquery/Makefile
echo x - science/dtiquery/distinfo
sed 's/^X//' >science/dtiquery/distinfo << 'END-of-science/dtiquery/distinfo'
XMD5 (dtiquery-1.1.tar.gz) = 4104aece50029d9b3183a244c2bb36fe
XSHA256 (dtiquery-1.1.tar.gz) = c59f5911e633f1f364cfd03ed18c296f99963184e2c2ddea937109f45f4b456e
XSIZE (dtiquery-1.1.tar.gz) = 285780
END-of-science/dtiquery/distinfo
echo x - science/dtiquery/pkg-descr
sed 's/^X//' >science/dtiquery/pkg-descr << 'END-of-science/dtiquery/pkg-descr'
XDTI visualization software from Stanford.
X
XWWW: http://graphics.stanford.edu/projects/dti/
END-of-science/dtiquery/pkg-descr
exit

>Release-Note:
>Audit-Trail:
>Unformatted:

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