[med-svn] [bioimagesuite] 03/04: Re-add debian/ dir
Andreas Tille
tille at debian.org
Mon Nov 20 15:20:43 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bioimagesuite.
commit 9983158c977fc960e794203787ee95da413e0fe2
Author: Andreas Tille <tille at debian.org>
Date: Mon Nov 20 18:17:03 2017 +0100
Re-add debian/ dir
---
debian/bioimagesuite-data.dirs | 1 +
debian/bioimagesuite-data.install | 1 +
debian/bioimagesuite.dirs | 3 +
debian/bioimagesuite.examples | 1 +
debian/bioimagesuite.install | 12 ++++
debian/bioimagesuite.links | 1 +
debian/bioimagesuite.lintian-overrides | 2 +
debian/bioimagesuite.menu | 5 ++
debian/changelog | 8 +++
debian/compat | 1 +
debian/control | 67 +++++++++++++++++++++++
debian/copyright | 33 +++++++++++
debian/get-orig-source | 23 ++++++++
debian/libbioimagesuite2.dirs | 2 +
debian/libbioimagesuite2.install | 1 +
debian/libbioimagesuite2.lintian-overrides | 33 +++++++++++
debian/libbioimagesuite2.postinst | 26 +++++++++
debian/libbioimagesuite2.shlibs.local | 19 +++++++
debian/old/README.Debian | 6 ++
debian/old/bioimagesuite-dev.dirs | 1 +
debian/old/bioimagesuite-dev.install | 1 +
debian/old/control.old | 63 +++++++++++++++++++++
debian/old/libbioimagesuite-dev.install | 1 +
debian/patches/edit_paths.patch | 88 ++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 74 +++++++++++++++++++++++++
debian/upstream/metadata | 30 ++++++++++
27 files changed, 504 insertions(+)
diff --git a/debian/bioimagesuite-data.dirs b/debian/bioimagesuite-data.dirs
new file mode 100644
index 0000000..db64484
--- /dev/null
+++ b/debian/bioimagesuite-data.dirs
@@ -0,0 +1 @@
+usr/share/bioimagesuite/
diff --git a/debian/bioimagesuite-data.install b/debian/bioimagesuite-data.install
new file mode 100644
index 0000000..97ef45e
--- /dev/null
+++ b/debian/bioimagesuite-data.install
@@ -0,0 +1 @@
+images/ usr/share/bioimagesuite/
diff --git a/debian/bioimagesuite.dirs b/debian/bioimagesuite.dirs
new file mode 100644
index 0000000..75e34d8
--- /dev/null
+++ b/debian/bioimagesuite.dirs
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/bioimagesuite
+#usr/share/lintian/overrides
diff --git a/debian/bioimagesuite.examples b/debian/bioimagesuite.examples
new file mode 100644
index 0000000..0bbe99e
--- /dev/null
+++ b/debian/bioimagesuite.examples
@@ -0,0 +1 @@
+example/*
diff --git a/debian/bioimagesuite.install b/debian/bioimagesuite.install
new file mode 100644
index 0000000..d42af89
--- /dev/null
+++ b/debian/bioimagesuite.install
@@ -0,0 +1,12 @@
+apps/ usr/lib/bioimagesuite/
+base/ usr/lib/bioimagesuite/
+datatree/ usr/lib/bioimagesuite/
+#lib/ usr/lib/bioimagesuite/
+main/ usr/lib/bioimagesuite/
+mjack/ usr/lib/bioimagesuite/
+
+setpaths.sh usr/lib/bioimagesuite/
+surfaceeditor usr/lib/bioimagesuite/
+setpaths.csh usr/lib/bioimagesuite/
+
+start_bioimagesuite usr/lib/bioimagesuite/
diff --git a/debian/bioimagesuite.links b/debian/bioimagesuite.links
new file mode 100644
index 0000000..0c6c20a
--- /dev/null
+++ b/debian/bioimagesuite.links
@@ -0,0 +1 @@
+usr/lib/bioimagesuite/start_bioimagesuite usr/bin/bioimagesuite
diff --git a/debian/bioimagesuite.lintian-overrides b/debian/bioimagesuite.lintian-overrides
new file mode 100644
index 0000000..6ca3c7a
--- /dev/null
+++ b/debian/bioimagesuite.lintian-overrides
@@ -0,0 +1,2 @@
+#bioimagesuite: shell-script-fails-syntax-check ./usr/lib/bioimagesuite/datatree/packages/ImageDialog.tcl
+#bioimagesuite: shell-script-fails-syntax-check ./usr/lib/bioimagesuite/datatree/packages/chellyDB.tcl
diff --git a/debian/bioimagesuite.menu b/debian/bioimagesuite.menu
new file mode 100644
index 0000000..e1224c7
--- /dev/null
+++ b/debian/bioimagesuite.menu
@@ -0,0 +1,5 @@
+?package(bioimagesuite):\
+ needs="X11" \
+ section="Applications/Science/Medicine" \
+ title="BioImageSuite" \
+ command="/usr/bin/bioimagesuite"
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5fe1241
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,8 @@
+bioimagesuite (2.0-1) UNRELEASED; urgency=low
+
+ DOESN'T EVEN COMPILE. (Check dpkg-shlibs note in debian/rules)
+
+ * Initial release
+ * Updated to Standards-Version 3.7.3 (no changes needed)
+
+ -- David Paleino <d.paleino at gmail.com> Wed, 06 Feb 2008 13:11:50 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7ed6ff8
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+5
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..edd78a5
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,67 @@
+Source: bioimagesuite
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 9), quilt, chrpath
+Standards-Version: 3.9.3
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bioimagesuite.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/bioimagesuite.git
+Homepage: http://www.bioimagesuite.org
+
+Package: bioimagesuite
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, itk3.1, vtk-tcl, libmetakit-tcl,
+ tcllib, iwidgets4, itcl3.1, libminc0, bioimagesuite-data, libxerces28,
+ minc-tools, hdf5-tools, netcdf-bin, libbioimagesuite2
+Description: integrated image analysis software suite
+ BioImage Suite has extensive capabilities for both neuro/cardiac
+ and abdominal image analysis and state of the art visualization.
+ Many packages are available that are highly extensible, and provide
+ functionality for image visualization and registration, surface
+ editing, cardiac 4D multi-slice editing, diffusion tensor image
+ processing, mouse segmentation and registration, and much more. It
+ can be integrated with other biomedical image processing software,
+ such as FSL and SPM. This site provides information, downloads,
+ documentation, and other resources for users of the software.
+ .
+ BioImage Suite was developed at Yale University and has been
+ extensively used at different labs at Yale since 2004.
+
+Package: bioimagesuite-data
+Architecture: all
+Description: integrated image analysis software suite
+ BioImage Suite has extensive capabilities for both neuro/cardiac
+ and abdominal image analysis and state of the art visualization.
+ Many packages are available that are highly extensible, and provide
+ functionality for image visualization and registration, surface
+ editing, cardiac 4D multi-slice editing, diffusion tensor image
+ processing, mouse segmentation and registration, and much more. It
+ can be integrated with other biomedical image processing software,
+ such as FSL and SPM. This site provides information, downloads,
+ documentation, and other resources for users of the software.
+ .
+ BioImage Suite was developed at Yale University and has been
+ extensively used at different labs at Yale since 2004.
+ .
+ This package contains architecture-independent data files.
+
+Package: libbioimagesuite2
+Architecture: any
+Section: libs
+Depends: ${shlibs:Depends}
+Description: integrated image analysis software suite
+ BioImage Suite has extensive capabilities for both neuro/cardiac
+ and abdominal image analysis and state of the art visualization.
+ Many packages are available that are highly extensible, and provide
+ functionality for image visualization and registration, surface
+ editing, cardiac 4D multi-slice editing, diffusion tensor image
+ processing, mouse segmentation and registration, and much more. It
+ can be integrated with other biomedical image processing software,
+ such as FSL and SPM. This site provides information, downloads,
+ documentation, and other resources for users of the software.
+ .
+ BioImage Suite was developed at Yale University and has been
+ extensively used at different labs at Yale since 2004.
+ .
+ This package contains library files.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..add3f8f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,33 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BioImageSuite
+Source: http://www.bioimagesuite.org/public/Downloads.html
+Comment: You need to login to download the source
+
+Files: *
+Copyright: © 2001-2011 X. Papademetris, M. Jackowski, N. Rajeevan, H. Okuda,
+ R.T. Constable, L.H. Staib,
+ Section of Bioimaging Sciences, Dept. of Diagnostic Radiology,
+ Yale School of Medicine
+License: GPL-2+
+
+Files: debian/*
+Copyright: © 2007 David Paleino <d.paleino at gmail.com>
+License: GPL-2+
+
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'.
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..833930e
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,23 @@
+#!/bin/sh -e
+# This will download the original source tarball to ../tarballs
+TARDIR=`pwd`/../tarballs
+TARNAME=bioimagesuite_latest_Linux_g++32.tar.gz
+NAME=bioimagesuite
+
+mkdir -p "$TARDIR"
+wget --user anonymous --password bioimagesuite \
+ http://www.bioimagesuite.org/download/linux_gcc32/${TARNAME} \
+ -P "$TARDIR"
+
+# Obtain upstream version number from changelog
+# Unfortunately upstream does not maintain version numbers in their
+# tarball. So we have to relay on the correct version number in
+# debian/changelog
+version=`dpkg-parsechangelog | grep "^Version:" | sed -e "s/^Version:[[:space:]]\+\([\.0-9]\+\)-*[0-9]*[[:space:]]*/\1/"`
+
+# rebuild the tarball
+cd "$TARDIR"
+tar -xzf ${TARNAME}
+mv ${NAME} ${NAME}-${version}
+GZIP="--best --no-name" tar -czf ${NAME}_${version}.orig.tar.gz ${NAME}-${version}
+rm -rf ${NAME}-${version} ${TARNAME}
diff --git a/debian/libbioimagesuite2.dirs b/debian/libbioimagesuite2.dirs
new file mode 100644
index 0000000..28aa8e0
--- /dev/null
+++ b/debian/libbioimagesuite2.dirs
@@ -0,0 +1,2 @@
+usr/lib
+#usr/share/lintian/overrides
diff --git a/debian/libbioimagesuite2.install b/debian/libbioimagesuite2.install
new file mode 100644
index 0000000..51003b4
--- /dev/null
+++ b/debian/libbioimagesuite2.install
@@ -0,0 +1 @@
+lib/* usr/lib/
diff --git a/debian/libbioimagesuite2.lintian-overrides b/debian/libbioimagesuite2.lintian-overrides
new file mode 100644
index 0000000..af532dd
--- /dev/null
+++ b/debian/libbioimagesuite2.lintian-overrides
@@ -0,0 +1,33 @@
+#libbioimagesuite2: several-sonames-in-same-package libvtkmpjCommonTCL.so libvtkmpjDiffusionTCL.so libvtkmpjGraphicsTCL.so libvtkmpjLevelsetTCL.so libvtknrCommonTCL.so libvtknrGraphicsTCL.so libvtknrImagingTCL.so libvtknrNmrlibTCL.so libvtkpxClosedTCL.so libvtkpxCommonTCL.so libvtkpxGUITCL.so libvtkpxGraphicsTCL.so libvtkpxImagingTCL.so libvtkpxLegacyTCL.so libvtkpxLevelsetTCL.so libvtkpxNmrlibTCL.so libvtkpxRegistrationTCL.so libvtkpxSegmentationTCL.so
+
+#libbioimagesuite2: package-name-doesnt-match-sonames libvtkmpjCommonTCL libvtkmpjDiffusionTCL libvtkmpjGraphicsTCL libvtkmpjLevelsetTCL libvtknrCommonTCL libvtknrGraphicsTCL libvtknrImagingTCL libvtknrNmrlibTCL libvtkpxClosedTCL libvtkpxCommonTCL libvtkpxGUITCL libvtkpxGraphicsTCL libvtkpxImagingTCL libvtkpxLegacyTCL libvtkpxLevelsetTCL libvtkpxNmrlibTCL libvtkpxRegistrationTCL libvtkpxSegmentationTCL
+
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtknrCommonTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxLevelsetTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxLegacyTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkmpjCommonTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkmpjDiffusionTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtknrNmrlibTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxNmrlibTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtknrGraphicsTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxImagingTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxCommonTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxSegmentationTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxRegistrationTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxClosedTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxGraphicsTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkmpjGraphicsTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkmpjLevelsetTCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtkpxGUITCL.so
+#libbioimagesuite2: no-shlibs-control-file usr/lib/libvtknrImagingTCL.so
+
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtknrCommonTCL.so
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtkpxClosedTCL.so
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtknrNmrlibTCL.so
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtkpxNmrlibTCL.so
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtkpxCommonTCL.so
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtkpxRegistrationTCL.so
+#libbioimagesuite2: shlib-with-non-pic-code usr/lib/libvtkpxGUITCL.so
+
+#libbioimagesuite2: shlib-with-executable-stack usr/lib/libvtkpxClosedTCL.so
+#libbioimagesuite2: shlib-with-executable-stack usr/lib/libvtkpxCommonTCL.so
diff --git a/debian/libbioimagesuite2.postinst b/debian/libbioimagesuite2.postinst
new file mode 100644
index 0000000..5e337c3
--- /dev/null
+++ b/debian/libbioimagesuite2.postinst
@@ -0,0 +1,26 @@
+#!/bin/sh
+# postinst script for bioimagesuite
+#
+# see: dh_installdeb(1)
+
+set -e
+
+case "$1" in
+ configure)
+ if [ -x /sbin/ldconfig ]
+ then
+ /sbin/ldconfig
+ fi
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+#DEBHELPER#
+
+exit 0
+
+
diff --git a/debian/libbioimagesuite2.shlibs.local b/debian/libbioimagesuite2.shlibs.local
new file mode 100644
index 0000000..0d10b20
--- /dev/null
+++ b/debian/libbioimagesuite2.shlibs.local
@@ -0,0 +1,19 @@
+#libbioimagesuite2 2 bioimagesuite (>= 2.0-1)
+libvtkmpjCommonTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkmpjDiffusionTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkmpjGraphicsTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkmpjLevelsetTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtknrCommonTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtknrGraphicsTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtknrImagingTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtknrNmrlibTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxClosedTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxCommonTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxGUITCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxGraphicsTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxImagingTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxLegacyTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxLevelsetTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxNmrlibTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxRegistrationTCL 2 libbioimagesuite2 (>= 2.0-1)
+libvtkpxSegmentationTCL 2 libbioimagesuite2 (>= 2.0-1)
diff --git a/debian/old/README.Debian b/debian/old/README.Debian
new file mode 100644
index 0000000..8d825a3
--- /dev/null
+++ b/debian/old/README.Debian
@@ -0,0 +1,6 @@
+bioimagesuite for Debian
+------------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- David Paleino <d.paleino at gmail.com> Fri, 26 Oct 2007 22:12:21 +0200
diff --git a/debian/old/bioimagesuite-dev.dirs b/debian/old/bioimagesuite-dev.dirs
new file mode 100644
index 0000000..4b49768
--- /dev/null
+++ b/debian/old/bioimagesuite-dev.dirs
@@ -0,0 +1 @@
+usr/include/bioimagesuite
diff --git a/debian/old/bioimagesuite-dev.install b/debian/old/bioimagesuite-dev.install
new file mode 100644
index 0000000..d380444
--- /dev/null
+++ b/debian/old/bioimagesuite-dev.install
@@ -0,0 +1 @@
+include/* usr/include/bioimagesuite/
diff --git a/debian/old/control.old b/debian/old/control.old
new file mode 100644
index 0000000..a5e2f39
--- /dev/null
+++ b/debian/old/control.old
@@ -0,0 +1,63 @@
+Source: bioimagesuite
+Section: science
+Priority: optional
+Maintainer: David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5)
+Standards-Version: 3.7.2
+Homepage: http://www.bioimagesuite.org
+
+Package: bioimagesuite
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, itk3.1, libvtk5, libmetakit-tcl,
+ tcllib, iwidgets4, itcl3.1, libminc0, bioimagesuite-dev
+Description: integrated image analysis suite
+ BioImage Suite is an integrated image analysis software suite developed at
+ Yale University.
+ .
+ BioImage Suite has been published as:
+ X. Papademetris, M. Jackowski, N. Rajeevan, H. Okuda, R.T. Constable, and L.H
+ Staib. BioImage Suite: An integrated medical image analysis suite,
+ Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale
+ School of Medicine. http://www.bioimagesuite.org .
+
+Package: bioimagesuite-dev
+Architecture: any
+Description: integrated image analysis suite - development headers
+ BioImage Suite is an integrated image analysis software suite developed at
+ Yale University.
+ .
+ BioImage Suite has been published as:
+ X. Papademetris, M. Jackowski, N. Rajeevan, H. Okuda, R.T. Constable, and L.H
+ Staib. BioImage Suite: An integrated medical image analysis suite,
+ Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale
+ School of Medicine. http://www.bioimagesuite.org .
+ .
+ This package contains the development header files.
+
+Package: bioimagesuite-data
+Architecture: all
+Description: integrated image analysis suite - common data files
+ BioImage Suite is an integrated image analysis software suite developed at
+ Yale University.
+ .
+ BioImage Suite has been published as:
+ X. Papademetris, M. Jackowski, N. Rajeevan, H. Okuda, R.T. Constable, and L.H
+ Staib. BioImage Suite: An integrated medical image analysis suite,
+ Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale
+ School of Medicine. http://www.bioimagesuite.org .
+ .
+ This package contains architecture-independent data files.
+
+Package: bioimagesuite-libs
+Architecture: any
+Description: integrated image analysis suite - library files
+ BioImage Suite is an integrated image analysis software suite developed at
+ Yale University.
+ .
+ BioImage Suite has been published as:
+ X. Papademetris, M. Jackowski, N. Rajeevan, H. Okuda, R.T. Constable, and L.H
+ Staib. BioImage Suite: An integrated medical image analysis suite,
+ Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale
+ School of Medicine. http://www.bioimagesuite.org .
+ .
+ This package contains library files.
diff --git a/debian/old/libbioimagesuite-dev.install b/debian/old/libbioimagesuite-dev.install
new file mode 100644
index 0000000..5f446b0
--- /dev/null
+++ b/debian/old/libbioimagesuite-dev.install
@@ -0,0 +1 @@
+lib/*.a usr/lib/bioimagesuite/
diff --git a/debian/patches/edit_paths.patch b/debian/patches/edit_paths.patch
new file mode 100644
index 0000000..65e3515
--- /dev/null
+++ b/debian/patches/edit_paths.patch
@@ -0,0 +1,88 @@
+Index: bioimagesuite-2.0/setpaths.csh
+===================================================================
+--- bioimagesuite-2.0.orig/setpaths.csh 2007-11-01 13:39:12.000000000 +0100
++++ bioimagesuite-2.0/setpaths.csh 2007-11-01 13:40:21.000000000 +0100
+@@ -1,23 +1,14 @@
++#!/bin/sh
+ #Script file to set paths for bioimagesuite
+
+ # Temp fix
+-setenv BASE /usr/local/bioimagesuite
++setenv BASE /usr/lib/bioimagesuite
+ setenv OS `uname`
+
+-if ( $OS == "Darwin") then
+- if (${?DISPLAY}) then
+- source /usr/local/vtk44_x11_yale/setvtk44.csh
+- else
+- source /usr/local/vtk44_carbon_yale/setvtk44.csh
+- endif
+-else
+- source /usr/local/vtk44_yale/setvtk44.csh
+-endif
++source /usr/local/vtk44_yale/setvtk44.csh
+
+ source /usr/local/itk241_yale/setitk241.csh
+
+-if (-r /usr/local/bioimagesuite_extra/setextra.csh ) source /usr/local/bioimagesuite_extra/setextra.csh
+-
+ setenv FSLDIR /usr/local/fsl
+ setenv FSLOUTPUTTYPE ANALYZE
+
+Index: bioimagesuite-2.0/setpaths.sh
+===================================================================
+--- bioimagesuite-2.0.orig/setpaths.sh 2007-11-01 13:39:12.000000000 +0100
++++ bioimagesuite-2.0/setpaths.sh 2007-11-01 13:40:21.000000000 +0100
+@@ -1,25 +1,14 @@
++#!/bin/sh
+ #Script file to set paths for bioimagesuite
+
+-BASE=/usr/local/bioimagesuite
++BASE=/usr/lib/bioimagesuite
+ OS=`uname`
+-if [ $OS == "Darwin" ]; then
+- if [ -n "$DISPLAY" ]; then
+- source /usr/local/vtk44_x11_yale/setvtk44.sh
+- else
+- source /usr/local/vtk44_carbon_yale/setvtk44.sh
+- fi
+-else
+- source /usr/local/vtk44_yale/setvtk44.sh
+-fi
+-
+
++source /usr/local/vtk44_yale/setvtk44.sh
+
+ source /usr/local/itk241_yale/setitk241.sh
+
+
+-if [ -r /usr/local/bioimagesuite_extra/setextra.sh ]; then
+- source /usr/local/bioimagesuite_extra/setextra.sh
+- fi
+
+
+ FSLDIR=/usr/local/fsl
+Index: bioimagesuite-2.0/start_bioimagesuite
+===================================================================
+--- bioimagesuite-2.0.orig/start_bioimagesuite 2007-11-01 13:39:12.000000000 +0100
++++ bioimagesuite-2.0/start_bioimagesuite 2007-11-01 13:40:21.000000000 +0100
+@@ -1,6 +1,5 @@
+ #!/bin/sh
+
+-BASE=/usr/local/bioimagesuite
++BASE=/usr/lib/bioimagesuite
+ source ${BASE}/setpaths.sh
+ pxmenu.tcl
+-
+Index: bioimagesuite-2.0/surfaceeditor
+===================================================================
+--- bioimagesuite-2.0.orig/surfaceeditor 2007-11-02 18:58:54.000000000 +0100
++++ bioimagesuite-2.0/surfaceeditor 2007-11-02 18:58:59.000000000 +0100
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+
+-BASE=/usr/local/bioimagesuite
++BASE=/usr/lib/bioimagesuite
+ source ${BASE}/setpaths.sh
+ pxitclsurfaceeditor.tcl
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..98c61a6
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+edit_paths.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..f5bf7ae
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,74 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/quilt/quilt.make
+
+build: patch build-stamp
+build-stamp:
+ dh_testdir
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+
+ dh_clean build-stamp
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ dh_install
+
+ # Removing RPATH...
+ chrpath -d $(CURDIR)/debian/libbioimagesuite2/usr/lib/*.so
+
+ # Fixing permissions...
+ chmod -R a-x $(CURDIR)/debian/bioimagesuite-data/usr/share/bioimagesuite/images/*
+
+ # Installing Lintian overrides
+# install -m 644 \
+# debian/libbioimagesuite2.lintian-override \
+# $(CURDIR)/debian/libbioimagesuite2/usr/share/lintian/overrides/libbioimagesuite2
+
+# install -m 644 \
+# debian/bioimagesuite.lintian-override \
+# $(CURDIR)/debian/bioimagesuite/usr/share/lintian/overrides/bioimagesuite
+
+binary-common: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+# dh_install
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_makeshlibs
+ # PLEASE FIX THIS:
+ # dpkg-shlibdeps: failure: couldn't find library libvtkCommonTCL.so
+ # (note: only packages with 'shlibs' files are looked into).
+ #dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary-indep: binary-common
+binary-arch: binary-common
+
+binary: binary-indep binary-arch
+
+get-orig-source:
+ # This will download the original source tarball
+ # to ../tarballs
+ sh debian/get-orig-source
+
+.PHONY: build clean binary-indep binary-arch binary install
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..60b9202
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,30 @@
+Reference:
+ - Author: X. Papademetris and M. Jackowski and N. Rajeevan and R. T. Constable and L. Staib
+ Title: "BioImage Suite: An integrated medical image analysis suite"
+ Journal: Insight Journal
+ Year: 2005
+ URL: http://hdl.handle.net/1926/37
+ eprint: http://www.insight-journal.org/download/viewpdf/30/101/bitstream
+ - Author: Alark Joshi and Dustin Scheinost and Hirohito Okuda and Dominique Belhachemi and Isabella Murphy and Lawrence H Staib and Xenophon Papademetris
+ Title: "Unified framework for development, deployment and robust testing of neuroimaging algorithms"
+ Journal: Neuroinformatics
+ Year: 2011
+ Volume: 9
+ Number: 1
+ Pages: 69-84
+ DOI: 10.1007/s12021-010-9092-8
+ PMID: 21249532
+ URL: http://www.springerlink.com/content/m763304211482j8r/?MUD=MP
+ eprint: http://www.springerlink.com/content/m763304211482j8r/fulltext.pdf
+ - Author: Dustin Scheinost and Thomas Z Teisseyre and Marcello Distasio and Matthew N DeSalvo and Xenophon Papademetris and Hal Blumenfeld
+ Title: "New open-source ictal SPECT analysis method implemented in BioImage Suite"
+ Journal: Epilepsia
+ Year: 2010
+ Volume: 51
+ Number: 4
+ Pages: 703-7
+ DOI: 10.1111/j.1528-1167.2009.02425.x
+ PMID: 20074234
+ URL: http://onlinelibrary.wiley.com/doi/10.1111/j.1528-1167.2009.02425.x/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1111/j.1528-1167.2009.02425.x/pdf
+Other-References: http://www.bioimagesuite.org/public/Papers.html
--
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