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 <[email protected]> Sat, 23 Feb 2013 21:25:56 +0100 + +cytoscape (2.8.4-1) unstable; urgency=low + + * update from upstream + + -- Ivo Maintz <[email protected]> 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 <[email protected]> Tue, 17 Apr 2012 13:03:18 +0200 + +cytoscape (2.8.2-1) unstable; urgency=low + + * update from upstream + + -- Ivo Maintz <[email protected]> Mon, 16 Apr 2012 12:23:34 +0200 + +cytoscape (2.8.1-2) natty; urgency=low + + * added the missing menu entry + + -- Ivo Maintz <[email protected]> Fri, 12 Aug 2011 10:21:26 +0200 + +cytoscape (2.8.1-1) unstable; urgency=low + + * update from upstream + + -- Ivo Maintz <[email protected]> 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 <[email protected]> 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 <[email protected]> Tue, 23 Nov 2010 09:21:11 +0100 + +cytoscape (2.8.0-1) unstable; urgency=low + + * Update from upstream + + -- Ivo Maintz <[email protected]> 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 <[email protected]> Mon, 22 Nov 2010 17:20:38 +0100 + +cytoscape (2.6.3-1) unstable; urgency=low + + * New releasee + + -- Ivo Maintz <[email protected]> Thu, 12 Nov 2009 12:00:00 +0200 + +cytoscape (2.6.2-1) unstable; urgency=low + + * Initial release + + -- Ivo Maintz <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 <[email protected]>, +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 <[email protected]> + +--- +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 <[email protected]> + +--- +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
