[med-svn] r13078 - in trunk/packages: . cytoscape cytoscape/trunk cytoscape/trunk/debian cytoscape/trunk/debian/patches cytoscape/trunk/debian/source
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Sat Feb 23 21:01:51 UTC 2013
Author: ivomaintz-guest
Date: 2013-02-23 21:01:51 +0000 (Sat, 23 Feb 2013)
New Revision: 13078
Added:
trunk/packages/cytoscape/
trunk/packages/cytoscape/trunk/
trunk/packages/cytoscape/trunk/debian/
trunk/packages/cytoscape/trunk/debian/changelog
trunk/packages/cytoscape/trunk/debian/compat
trunk/packages/cytoscape/trunk/debian/control
trunk/packages/cytoscape/trunk/debian/copyright
trunk/packages/cytoscape/trunk/debian/cytoscape.1
trunk/packages/cytoscape/trunk/debian/cytoscape.desktop
trunk/packages/cytoscape/trunk/debian/cytoscape.docs
trunk/packages/cytoscape/trunk/debian/cytoscape.install
trunk/packages/cytoscape/trunk/debian/cytoscape.links
trunk/packages/cytoscape/trunk/debian/dirs
trunk/packages/cytoscape/trunk/debian/docs
trunk/packages/cytoscape/trunk/debian/get-orig-source
trunk/packages/cytoscape/trunk/debian/patches/
trunk/packages/cytoscape/trunk/debian/patches/MPL.patch
trunk/packages/cytoscape/trunk/debian/patches/series
trunk/packages/cytoscape/trunk/debian/patches/shell.patch
trunk/packages/cytoscape/trunk/debian/postinst
trunk/packages/cytoscape/trunk/debian/prerm
trunk/packages/cytoscape/trunk/debian/rules
trunk/packages/cytoscape/trunk/debian/source/
trunk/packages/cytoscape/trunk/debian/source/format
Log:
added cytoscape to the repository
Added: trunk/packages/cytoscape/trunk/debian/changelog
===================================================================
--- trunk/packages/cytoscape/trunk/debian/changelog (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/changelog 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,76 @@
+cytoscape (3.0-1) UNRELEASED; urgency=low
+
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Sat, 23 Feb 2013 21:25:56 +0100
+
+cytoscape (2.8.4-1) unstable; urgency=low
+
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Fri, 01 Feb 2013 11:51:59 +0100
+
+cytoscape (2.8.3-1) unstable; urgency=low
+
+ * update from upstream
+ * now we build cytoscape from scratch
+
+ -- Ivo Maintz <ivo at maintz.de> Tue, 17 Apr 2012 13:03:18 +0200
+
+cytoscape (2.8.2-1) unstable; urgency=low
+
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Mon, 16 Apr 2012 12:23:34 +0200
+
+cytoscape (2.8.1-2) natty; urgency=low
+
+ * added the missing menu entry
+
+ -- Ivo Maintz <ivo at maintz.de> Fri, 12 Aug 2011 10:21:26 +0200
+
+cytoscape (2.8.1-1) unstable; urgency=low
+
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Mon, 28 Feb 2011 12:12:37 +0100
+
+cytoscape (2.8.0-3) unstable; urgency=low
+
+ * bugfix fron upstream: cytoscapes regards the file /usr/share/cytoscape/Cytoscape.vmoptions
+
+ -- Ivo Maintz <ivo at maintz.de> Tue, 23 Nov 2010 09:57:25 +0100
+
+cytoscape (2.8.0-2) unstable; urgency=low
+
+ * bugfix; cytoscapes ignores the file /usr/share/cytoscape/Cytoscape.vmoptions
+ and only regards ~/.cytoscape/Cytoscape.vmoptions
+
+ -- Ivo Maintz <ivo at maintz.de> Tue, 23 Nov 2010 09:21:11 +0100
+
+cytoscape (2.8.0-1) unstable; urgency=low
+
+ * Update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Thu, 28 Sep 2010 13:25:00 +0200
+
+cytoscape (2.7.0-1) unstable; urgency=low
+
+ * Update from upstream
+ * bugfix; the file /usr/share/cytoscape/Cytoscape.vmoptions is now
+ generated during the install process, to get a properly working
+ cytoscape on i386 systems
+
+ -- Ivo Maintz <ivo at maintz.de> Mon, 22 Nov 2010 17:20:38 +0100
+
+cytoscape (2.6.3-1) unstable; urgency=low
+
+ * New releasee
+
+ -- Ivo Maintz <ivo at maintz.de> Thu, 12 Nov 2009 12:00:00 +0200
+
+cytoscape (2.6.2-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Ivo Maintz <ivo at maintz.de> Tue, 30 Jun 2009 16:16:52 +0200
Added: trunk/packages/cytoscape/trunk/debian/compat
===================================================================
--- trunk/packages/cytoscape/trunk/debian/compat (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/compat 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1 @@
+9
Added: trunk/packages/cytoscape/trunk/debian/control
===================================================================
--- trunk/packages/cytoscape/trunk/debian/control (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/control 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,22 @@
+Source: cytoscape
+Section: science
+Priority: extra
+Maintainer: Ivo Maintz <ivo at maintz.de>
+Build-Depends: debhelper (>= 9.0.0),
+ maven,
+ default-jdk
+Standards-Version: 3.9.3
+Homepage: http://www.cytoscape.org
+
+Package: cytoscape
+Architecture: all
+Depends: ${misc:Depends},
+ default-jre, jarwrapper
+Description: visualizing molecular interaction networks
+ Cytoscape is an open source bioinformatics software platform for visualizing
+ molecular interaction networks and biological pathways and integrating these
+ networks with annotations, gene expression profiles and other state data.
+ Although Cytoscape was originally designed for biological research, now it is
+ a general platform for complex network analysis and visualization.
+ Cytoscape core distribution provides a basic set of features for data
+ integration and visualization.
Added: trunk/packages/cytoscape/trunk/debian/copyright
===================================================================
--- trunk/packages/cytoscape/trunk/debian/copyright (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/copyright 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,19 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Cytoscape
+Source: http://chianti.ucsd.edu/svn/cytoscape/trunk
+
+Files: *
+Copyright: 2001-2012 Cytoscape Consortium
+License: LGPL-2.1
+
+Files: debian/*
+Copyright: 2012 Ivo Maintz <ivo at maintz.de>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: LGPL-2.1
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2.1 can be found in "/usr/share/common-licenses/LGPL-2.1".
Added: trunk/packages/cytoscape/trunk/debian/cytoscape.1
===================================================================
--- trunk/packages/cytoscape/trunk/debian/cytoscape.1 (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/cytoscape.1 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,60 @@
+.TH cytoscape 1 "Februar 23, 2013" "" "cytoscape"
+
+.SH NAME
+cytoscape
+
+.SH SYNOPSIS
+.B cytoscape
+.RI [ OPTIONS ]
+.br
+
+.SH DESCRIPTION
+ Cytoscape is an open source bioinformatics software platform for visualizing
+ molecular interaction networks and biological pathways and integrating these
+ networks with annotations, gene expression profiles and other state data.
+ Although Cytoscape was originally designed for biological research, now it is
+ a general platform for complex network analysis and visualization.
+ Cytoscape core distribution provides a basic set of features for data
+ integration and visualization.
+.PP
+\fBcytoscape\fP is a software application for visualizing molecular interaction networks
+
+.SH OPTIONS
+.B
+.IP
+.B \-h, \-\-help
+ Print the help
+.IP
+.B \-v, \-\-version
+ Print the version number
+.IP
+.B \-s, \-\-session <file>
+ Load a cytoscape session (.cys) file
+.IP
+.B \-n,\-\-network <file>
+ Load a network file (any format)
+.IP
+.B \-s, \-\-edge-attrs <file>
+ Load an edge attributes file (edge attribute format)
+.IP
+.B \-n, \-\--node-attrs <file>
+ Load a node attributes file (node attribute format)
+.IP
+.B \-m, \-\-matrix <file>
+ Load a node attribute matrix file (table)
+.IP
+.B \-p, \-\-plugin <file>
+ Load a plugin jar file, directory of jar files, plugin class name, or plugin jar URL
+.IP
+.B \-P, \-\-props <file>
+ Load cytoscape properties file (Java properties format) or individual property: -P name=value
+.IP
+.B \-\-validate
+ Only validate the given input file (COPASI, Gepasi, or SBML) without performing any calculations.
+.IP
+.B \-V, \-\-vizmap <file>
+ Load vizmap properties file (Java properties format)
+
+.PP
+This manual page was written by Ivo Maintz <ivo at maintz.de>,
+for the Debian project (and may be used by others).
Added: trunk/packages/cytoscape/trunk/debian/cytoscape.desktop
===================================================================
--- trunk/packages/cytoscape/trunk/debian/cytoscape.desktop (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/cytoscape.desktop 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,9 @@
+[Desktop Entry]
+Name=Cytoscape
+Comment=visualizing molecular interaction networks
+Exec=/usr/bin/cytoscape
+Icon=/usr/share/icons/CytoscapeLogo.svg
+Terminal=false
+Type=Application
+Categories=Development;Science;Biology
+StartupNotify=true
Added: trunk/packages/cytoscape/trunk/debian/cytoscape.docs
===================================================================
--- trunk/packages/cytoscape/trunk/debian/cytoscape.docs (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/cytoscape.docs 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,2 @@
+distribution/target/cytoscape-*/cytoscape-*/sampleData
+distribution/target/cytoscape-*/cytoscape-*/docs/*
Added: trunk/packages/cytoscape/trunk/debian/cytoscape.install
===================================================================
--- trunk/packages/cytoscape/trunk/debian/cytoscape.install (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/cytoscape.install 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,7 @@
+distribution/target/cytoscape-*/cytoscape-*/plugins /usr/share/cytoscape
+distribution/target/cytoscape-*/cytoscape-*/Cytoscape.vmoptions /usr/share/cytoscape
+distribution/target/cytoscape-*/cytoscape-*/cytoscape.sh /usr/share/cytoscape
+distribution/target/cytoscape-*/cytoscape-*/gen_vmoptions.sh /usr/share/cytoscape
+distribution/target/cytoscape-*/cytoscape-*/cytoscape.jar /usr/share/cytoscape
+debian/cytoscape.desktop /usr/share/applications
+application/src/main/resources/cytoscape/images/CytoscapeLogo.svg /usr/share/icons/
Added: trunk/packages/cytoscape/trunk/debian/cytoscape.links
===================================================================
--- trunk/packages/cytoscape/trunk/debian/cytoscape.links (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/cytoscape.links 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,2 @@
+/usr/share/doc/cytoscape/sampleData /usr/share/cytoscape/sampleData
+/usr/share/cytoscape/cytoscape.sh /usr/bin/cytoscape
Added: trunk/packages/cytoscape/trunk/debian/dirs
===================================================================
--- trunk/packages/cytoscape/trunk/debian/dirs (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/dirs 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1 @@
+usr/share/cytoscape
Added: trunk/packages/cytoscape/trunk/debian/docs
===================================================================
--- trunk/packages/cytoscape/trunk/debian/docs (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/docs 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1 @@
+LICENSE.txt
Added: trunk/packages/cytoscape/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/cytoscape/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/get-orig-source 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,29 @@
+#!/bin/sh
+# get source for cytoscape from SVN because there is no source tarball distribution
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+ORIGNAME=cytoscape
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${ORIGNAME}_release.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+SVNTAG=`echo ${VERSION} | sed 's/\./_/g'`
+rm -f ../${ORIGNAME}_release_${SVNTAG}
+RELEASE=${ORIGNAME}_release_${SVNTAG}
+TARDIR=${NAME}-${VERSION}
+
+mkdir -p ../tarballs
+cd ../tarballs
+# svn export conserves time stamps of the files, checkout does not
+LC_ALL=C svn export http://chianti.ucsd.edu/svn/cytoscape/trunk ${TARDIR}
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}"
+rm -rf "${NAME}"-"$VERSION"
Property changes on: trunk/packages/cytoscape/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/cytoscape/trunk/debian/patches/MPL.patch
===================================================================
--- trunk/packages/cytoscape/trunk/debian/patches/MPL.patch (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/patches/MPL.patch 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,387 @@
+Description: added the text for the Mozilla Public License
+ .
+Author: Ivo Maintz <ivo at maintz.de>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Last-Update: <2013-02-01>
+
+--- /dev/null
++++ cytoscape-2.8.4distribution/src/main/licenses/MOZILLA_PUBLIC_LICENSE.txt
+@@ -0,0 +1,373 @@
++Mozilla Public License Version 2.0
++==================================
++
++1. Definitions
++--------------
++
++1.1. "Contributor"
++ means each individual or legal entity that creates, contributes to
++ the creation of, or owns Covered Software.
++
++1.2. "Contributor Version"
++ means the combination of the Contributions of others (if any) used
++ by a Contributor and that particular Contributor's Contribution.
++
++1.3. "Contribution"
++ means Covered Software of a particular Contributor.
++
++1.4. "Covered Software"
++ means Source Code Form to which the initial Contributor has attached
++ the notice in Exhibit A, the Executable Form of such Source Code
++ Form, and Modifications of such Source Code Form, in each case
++ including portions thereof.
++
++1.5. "Incompatible With Secondary Licenses"
++ means
++
++ (a) that the initial Contributor has attached the notice described
++ in Exhibit B to the Covered Software; or
++
++ (b) that the Covered Software was made available under the terms of
++ version 1.1 or earlier of the License, but not also under the
++ terms of a Secondary License.
++
++1.6. "Executable Form"
++ means any form of the work other than Source Code Form.
++
++1.7. "Larger Work"
++ means a work that combines Covered Software with other material, in
++ a separate file or files, that is not Covered Software.
++
++1.8. "License"
++ means this document.
++
++1.9. "Licensable"
++ means having the right to grant, to the maximum extent possible,
++ whether at the time of the initial grant or subsequently, any and
++ all of the rights conveyed by this License.
++
++1.10. "Modifications"
++ means any of the following:
++
++ (a) any file in Source Code Form that results from an addition to,
++ deletion from, or modification of the contents of Covered
++ Software; or
++
++ (b) any new file in Source Code Form that contains any Covered
++ Software.
++
++1.11. "Patent Claims" of a Contributor
++ means any patent claim(s), including without limitation, method,
++ process, and apparatus claims, in any patent Licensable by such
++ Contributor that would be infringed, but for the grant of the
++ License, by the making, using, selling, offering for sale, having
++ made, import, or transfer of either its Contributions or its
++ Contributor Version.
++
++1.12. "Secondary License"
++ means either the GNU General Public License, Version 2.0, the GNU
++ Lesser General Public License, Version 2.1, the GNU Affero General
++ Public License, Version 3.0, or any later versions of those
++ licenses.
++
++1.13. "Source Code Form"
++ means the form of the work preferred for making modifications.
++
++1.14. "You" (or "Your")
++ means an individual or a legal entity exercising rights under this
++ License. For legal entities, "You" includes any entity that
++ controls, is controlled by, or is under common control with You. For
++ purposes of this definition, "control" means (a) the power, direct
++ or indirect, to cause the direction or management of such entity,
++ whether by contract or otherwise, or (b) ownership of more than
++ fifty percent (50%) of the outstanding shares or beneficial
++ ownership of such entity.
++
++2. License Grants and Conditions
++--------------------------------
++
++2.1. Grants
++
++Each Contributor hereby grants You a world-wide, royalty-free,
++non-exclusive license:
++
++(a) under intellectual property rights (other than patent or trademark)
++ Licensable by such Contributor to use, reproduce, make available,
++ modify, display, perform, distribute, and otherwise exploit its
++ Contributions, either on an unmodified basis, with Modifications, or
++ as part of a Larger Work; and
++
++(b) under Patent Claims of such Contributor to make, use, sell, offer
++ for sale, have made, import, and otherwise transfer either its
++ Contributions or its Contributor Version.
++
++2.2. Effective Date
++
++The licenses granted in Section 2.1 with respect to any Contribution
++become effective for each Contribution on the date the Contributor first
++distributes such Contribution.
++
++2.3. Limitations on Grant Scope
++
++The licenses granted in this Section 2 are the only rights granted under
++this License. No additional rights or licenses will be implied from the
++distribution or licensing of Covered Software under this License.
++Notwithstanding Section 2.1(b) above, no patent license is granted by a
++Contributor:
++
++(a) for any code that a Contributor has removed from Covered Software;
++ or
++
++(b) for infringements caused by: (i) Your and any other third party's
++ modifications of Covered Software, or (ii) the combination of its
++ Contributions with other software (except as part of its Contributor
++ Version); or
++
++(c) under Patent Claims infringed by Covered Software in the absence of
++ its Contributions.
++
++This License does not grant any rights in the trademarks, service marks,
++or logos of any Contributor (except as may be necessary to comply with
++the notice requirements in Section 3.4).
++
++2.4. Subsequent Licenses
++
++No Contributor makes additional grants as a result of Your choice to
++distribute the Covered Software under a subsequent version of this
++License (see Section 10.2) or under the terms of a Secondary License (if
++permitted under the terms of Section 3.3).
++
++2.5. Representation
++
++Each Contributor represents that the Contributor believes its
++Contributions are its original creation(s) or it has sufficient rights
++to grant the rights to its Contributions conveyed by this License.
++
++2.6. Fair Use
++
++This License is not intended to limit any rights You have under
++applicable copyright doctrines of fair use, fair dealing, or other
++equivalents.
++
++2.7. Conditions
++
++Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
++in Section 2.1.
++
++3. Responsibilities
++-------------------
++
++3.1. Distribution of Source Form
++
++All distribution of Covered Software in Source Code Form, including any
++Modifications that You create or to which You contribute, must be under
++the terms of this License. You must inform recipients that the Source
++Code Form of the Covered Software is governed by the terms of this
++License, and how they can obtain a copy of this License. You may not
++attempt to alter or restrict the recipients' rights in the Source Code
++Form.
++
++3.2. Distribution of Executable Form
++
++If You distribute Covered Software in Executable Form then:
++
++(a) such Covered Software must also be made available in Source Code
++ Form, as described in Section 3.1, and You must inform recipients of
++ the Executable Form how they can obtain a copy of such Source Code
++ Form by reasonable means in a timely manner, at a charge no more
++ than the cost of distribution to the recipient; and
++
++(b) You may distribute such Executable Form under the terms of this
++ License, or sublicense it under different terms, provided that the
++ license for the Executable Form does not attempt to limit or alter
++ the recipients' rights in the Source Code Form under this License.
++
++3.3. Distribution of a Larger Work
++
++You may create and distribute a Larger Work under terms of Your choice,
++provided that You also comply with the requirements of this License for
++the Covered Software. If the Larger Work is a combination of Covered
++Software with a work governed by one or more Secondary Licenses, and the
++Covered Software is not Incompatible With Secondary Licenses, this
++License permits You to additionally distribute such Covered Software
++under the terms of such Secondary License(s), so that the recipient of
++the Larger Work may, at their option, further distribute the Covered
++Software under the terms of either this License or such Secondary
++License(s).
++
++3.4. Notices
++
++You may not remove or alter the substance of any license notices
++(including copyright notices, patent notices, disclaimers of warranty,
++or limitations of liability) contained within the Source Code Form of
++the Covered Software, except that You may alter any license notices to
++the extent required to remedy known factual inaccuracies.
++
++3.5. Application of Additional Terms
++
++You may choose to offer, and to charge a fee for, warranty, support,
++indemnity or liability obligations to one or more recipients of Covered
++Software. However, You may do so only on Your own behalf, and not on
++behalf of any Contributor. You must make it absolutely clear that any
++such warranty, support, indemnity, or liability obligation is offered by
++You alone, and You hereby agree to indemnify every Contributor for any
++liability incurred by such Contributor as a result of warranty, support,
++indemnity or liability terms You offer. You may include additional
++disclaimers of warranty and limitations of liability specific to any
++jurisdiction.
++
++4. Inability to Comply Due to Statute or Regulation
++---------------------------------------------------
++
++If it is impossible for You to comply with any of the terms of this
++License with respect to some or all of the Covered Software due to
++statute, judicial order, or regulation then You must: (a) comply with
++the terms of this License to the maximum extent possible; and (b)
++describe the limitations and the code they affect. Such description must
++be placed in a text file included with all distributions of the Covered
++Software under this License. Except to the extent prohibited by statute
++or regulation, such description must be sufficiently detailed for a
++recipient of ordinary skill to be able to understand it.
++
++5. Termination
++--------------
++
++5.1. The rights granted under this License will terminate automatically
++if You fail to comply with any of its terms. However, if You become
++compliant, then the rights granted under this License from a particular
++Contributor are reinstated (a) provisionally, unless and until such
++Contributor explicitly and finally terminates Your grants, and (b) on an
++ongoing basis, if such Contributor fails to notify You of the
++non-compliance by some reasonable means prior to 60 days after You have
++come back into compliance. Moreover, Your grants from a particular
++Contributor are reinstated on an ongoing basis if such Contributor
++notifies You of the non-compliance by some reasonable means, this is the
++first time You have received notice of non-compliance with this License
++from such Contributor, and You become compliant prior to 30 days after
++Your receipt of the notice.
++
++5.2. If You initiate litigation against any entity by asserting a patent
++infringement claim (excluding declaratory judgment actions,
++counter-claims, and cross-claims) alleging that a Contributor Version
++directly or indirectly infringes any patent, then the rights granted to
++You by any and all Contributors for the Covered Software under Section
++2.1 of this License shall terminate.
++
++5.3. In the event of termination under Sections 5.1 or 5.2 above, all
++end user license agreements (excluding distributors and resellers) which
++have been validly granted by You or Your distributors under this License
++prior to termination shall survive termination.
++
++************************************************************************
++* *
++* 6. Disclaimer of Warranty *
++* ------------------------- *
++* *
++* Covered Software is provided under this License on an "as is" *
++* basis, without warranty of any kind, either expressed, implied, or *
++* statutory, including, without limitation, warranties that the *
++* Covered Software is free of defects, merchantable, fit for a *
++* particular purpose or non-infringing. The entire risk as to the *
++* quality and performance of the Covered Software is with You. *
++* Should any Covered Software prove defective in any respect, You *
++* (not any Contributor) assume the cost of any necessary servicing, *
++* repair, or correction. This disclaimer of warranty constitutes an *
++* essential part of this License. No use of any Covered Software is *
++* authorized under this License except under this disclaimer. *
++* *
++************************************************************************
++
++************************************************************************
++* *
++* 7. Limitation of Liability *
++* -------------------------- *
++* *
++* Under no circumstances and under no legal theory, whether tort *
++* (including negligence), contract, or otherwise, shall any *
++* Contributor, or anyone who distributes Covered Software as *
++* permitted above, be liable to You for any direct, indirect, *
++* special, incidental, or consequential damages of any character *
++* including, without limitation, damages for lost profits, loss of *
++* goodwill, work stoppage, computer failure or malfunction, or any *
++* and all other commercial damages or losses, even if such party *
++* shall have been informed of the possibility of such damages. This *
++* limitation of liability shall not apply to liability for death or *
++* personal injury resulting from such party's negligence to the *
++* extent applicable law prohibits such limitation. Some *
++* jurisdictions do not allow the exclusion or limitation of *
++* incidental or consequential damages, so this exclusion and *
++* limitation may not apply to You. *
++* *
++************************************************************************
++
++8. Litigation
++-------------
++
++Any litigation relating to this License may be brought only in the
++courts of a jurisdiction where the defendant maintains its principal
++place of business and such litigation shall be governed by laws of that
++jurisdiction, without reference to its conflict-of-law provisions.
++Nothing in this Section shall prevent a party's ability to bring
++cross-claims or counter-claims.
++
++9. Miscellaneous
++----------------
++
++This License represents the complete agreement concerning the subject
++matter hereof. If any provision of this License is held to be
++unenforceable, such provision shall be reformed only to the extent
++necessary to make it enforceable. Any law or regulation which provides
++that the language of a contract shall be construed against the drafter
++shall not be used to construe this License against a Contributor.
++
++10. Versions of the License
++---------------------------
++
++10.1. New Versions
++
++Mozilla Foundation is the license steward. Except as provided in Section
++10.3, no one other than the license steward has the right to modify or
++publish new versions of this License. Each version will be given a
++distinguishing version number.
++
++10.2. Effect of New Versions
++
++You may distribute the Covered Software under the terms of the version
++of the License under which You originally received the Covered Software,
++or under the terms of any subsequent version published by the license
++steward.
++
++10.3. Modified Versions
++
++If you create software not governed by this License, and you want to
++create a new license for such software, you may create and use a
++modified version of this License if you rename the license and remove
++any references to the name of the license steward (except to note that
++such modified license differs from this License).
++
++10.4. Distributing Source Code Form that is Incompatible With Secondary
++Licenses
++
++If You choose to distribute Source Code Form that is Incompatible With
++Secondary Licenses under the terms of this version of the License, the
++notice described in Exhibit B of this License must be attached.
++
++Exhibit A - Source Code Form License Notice
++-------------------------------------------
++
++ This Source Code Form is subject to the terms of the Mozilla Public
++ License, v. 2.0. If a copy of the MPL was not distributed with this
++ file, You can obtain one at http://mozilla.org/MPL/2.0/.
++
++If it is not possible or desirable to put the notice in a particular
++file, then You may include the notice in a location (such as a LICENSE
++file in a relevant directory) where a recipient would be likely to look
++for such a notice.
++
++You may add additional accurate notices of copyright ownership.
++
++Exhibit B - "Incompatible With Secondary Licenses" Notice
++---------------------------------------------------------
++
++ This Source Code Form is "Incompatible With Secondary Licenses", as
++ defined by the Mozilla Public License, v. 2.0.
Added: trunk/packages/cytoscape/trunk/debian/patches/series
===================================================================
--- trunk/packages/cytoscape/trunk/debian/patches/series (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/patches/series 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,2 @@
+MPL.patch
+shell.patch
Added: trunk/packages/cytoscape/trunk/debian/patches/shell.patch
===================================================================
--- trunk/packages/cytoscape/trunk/debian/patches/shell.patch (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/patches/shell.patch 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,25 @@
+Description: repaired the handling of a softlinked startup script
+ .
+Author: Ivo Maintz <ivo at maintz.de>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Last-Update: <2013-02-01>
+
+--- cytoscape-2.8.4.orig/distribution/src/main/bin/cytoscape.sh
++++ cytoscape-2.8.4/distribution/src/main/bin/cytoscape.sh
+@@ -4,10 +4,7 @@
+ # This script is a UNIX-only (i.e. Linux, Mac OS, etc.) version
+ #-------------------------------------------------------------------------------
+
+-script_path="$(dirname -- $0)"
+-if [ -h $script_path ]; then
+- script_path="$(readlink $script_path)"
+-fi
++script_path="$(dirname $(readlink -f $0))"
+
+ #vm_options_path=$HOME/.cytoscape
+ vm_options_path=$script_path
Added: trunk/packages/cytoscape/trunk/debian/postinst
===================================================================
--- trunk/packages/cytoscape/trunk/debian/postinst (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/postinst 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,28 @@
+#!/bin/bash
+# postinst script for cytoscape
+#
+# see: dh_installdeb(1)
+
+set -e
+
+case "$1" in
+ configure)
+ cd /usr/share/cytoscape
+ ./gen_vmoptions.sh
+
+ ;;
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/cytoscape/trunk/debian/prerm
===================================================================
--- trunk/packages/cytoscape/trunk/debian/prerm (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/prerm 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,33 @@
+#!/bin/sh
+# prerm script for cytoscape
+#
+# see: dh_installdeb(1)
+
+set -e
+
+case "$1" in
+ remove)
+ rm -f /usr/share/cytoscape/*ytoscape.vmoptions
+ ;;
+
+ purge)
+ ;;
+
+ upgrade|failed-upgrade|disappear)
+ ;;
+
+ abort-install|abort-upgrade)
+ ;;
+
+ *)
+ echo "$0 called with unknown argument \`$1'" 1>&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/cytoscape/trunk/debian/rules
===================================================================
--- trunk/packages/cytoscape/trunk/debian/rules (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/rules 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ mvn clean -Dmaven.repo.local=${CURDIR}/../mvntmp
+ rm -f pwMexVersion.p
+
+override_dh_auto_build:
+ mvn install -Dmaven.test.skip=true -Dmaven.repo.local=${CURDIR}/../mvntmp
+ chmod -x distribution/target/cytoscape*/cytoscape*/Cytoscape.vmoptions
+ find distribution/target/cytoscape-*/cytoscape-* -name "*.jar" -exec chmod -x {} +
+
+get-orig-source:
+ debian/get-orig-source
Property changes on: trunk/packages/cytoscape/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/cytoscape/trunk/debian/source/format
===================================================================
--- trunk/packages/cytoscape/trunk/debian/source/format (rev 0)
+++ trunk/packages/cytoscape/trunk/debian/source/format 2013-02-23 21:01:51 UTC (rev 13078)
@@ -0,0 +1 @@
+3.0 (quilt)
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