Date: Tue, 29 Jan 2008 15:43:50 -0600 (CST) From: Jason Bacon <bacon@smithers.neuro.mcw.edu> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/120129: New port: science/dtiquery DTI Visualization Software Message-ID: <200801292143.m0TLho9T036175@smithers.neuro.mcw.edu> Resent-Message-ID: <200801292150.m0TLo2aZ089408@freefall.freebsd.org>
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>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@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@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@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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