[med-svn] r11754 - trunk/packages/rostlab/predictprotein/trunk/debian
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Jul 12 10:21:22 UTC 2012
Author: lkajan-guest
Date: 2012-07-12 10:21:22 +0000 (Thu, 12 Jul 2012)
New Revision: 11754
Added:
trunk/packages/rostlab/predictprotein/trunk/debian/upstream
Modified:
trunk/packages/rostlab/predictprotein/trunk/debian/changelog
trunk/packages/rostlab/predictprotein/trunk/debian/control
trunk/packages/rostlab/predictprotein/trunk/debian/copyright
trunk/packages/rostlab/predictprotein/trunk/debian/watch
Log:
merged duplicated repositories
Modified: trunk/packages/rostlab/predictprotein/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/changelog 2012-07-12 10:13:16 UTC (rev 11753)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/changelog 2012-07-12 10:21:22 UTC (rev 11754)
@@ -3,7 +3,7 @@
* [lkajan at rostlab.org] PLEASE DO NOT UPLOAD
RELEASED FOR ROST LAB (NOT YET FOR THE WORLD)
- * New upstream release
+ * Initial release (Closes: #680610)
-- Laszlo Kajan <lkajan at rostlab.org> Mon, 09 Jul 2012 14:42:39 +0200
Modified: trunk/packages/rostlab/predictprotein/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/control 2012-07-12 10:13:16 UTC (rev 11753)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/control 2012-07-12 10:21:22 UTC (rev 11754)
@@ -1,29 +1,37 @@
Source: predictprotein
-Section: non-free/science
+Section: science
Priority: extra
-Maintainer: Guy Yachdav <gyachdav at rostlab.org>
-Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 8), autotools-dev, po-debconf
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Guy Yachdav <gyachdav at rostlab.org>, Laszlo Kajan <lkajan at rostlab.org>, Simon Domke <domkes at in.tum.de>
+Build-Depends: debhelper (>= 8)
Standards-Version: 3.9.3
Homepage: http://www.predictprotein.org
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/predictprotein/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/predictprotein/trunk/
+DM-Upload-Allowed: yes
Package: predictprotein
Architecture: all
-Pre-Depends: debconf (>= 0.5)
-Depends: ${shlibs:Depends}, ${misc:Depends}, blast2, bioperl, ncoils (>= 2002-3), disulfinder, hmmer (>= 3.0), hmmer2, librg-liu-bundle-perl, librg-pp-bundle-perl (>= 1.0.21), librg-utils-perl (>= 1.0.24), ncbi-seg, make, norsnet, norsp, perl, predictnls, profbval (>= 1.0.15), profisis, profphd, proftmb (>= 1.1.9-1)
+Depends: ${misc:Depends}, blast2, bioperl, ncoils (>= 2002-3), disulfinder, hmmer (>= 3.0), hmmer2, librg-liu-bundle-perl, librg-pp-bundle-perl (>= 1.0.21), librg-utils-perl (>= 1.0.24), ncbi-seg, make, norsnet, norsp, perl, predictnls, profbval (>= 1.0.15), profisis, profphd, proftmb (>= 1.1.9-1)
Recommends: pp-popularity-contest
Suggests: pp-cache-mgr (>= 1.0.3), predictprotein-nonfree
Description: suite of protein sequence analysis tools
PredictProtein is a sequence analysis suite providing prediction of protein
- structure and function. It takes protein sequences or alignments as input
- and provides the following per-residue or whole protein annotations: multiple
- sequence alignments, PROSITE sequence motifs, low-complexity regions, nuclear
- localisation signals, regions lacking regular structure (NORS), secondary
- structure, solvent accessibility, transmembrane helices,
- coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular
- localization, disordered regions, B-value flexibility, protein-protein
- interaction sites and protein-DNA interaction sites. Upon request fold
- recognition by prediction-based threading, predictions of transmembrane
- strands and inter-residue contacts are also available.
+ structure and function.
+ .
+ PredictProtein takes a protein sequence as input and provides the following
+ per-residue, or whole protein annotations:
+ * secondary structure
+ * solvent accessibility
+ * multiple sequence alignments
+ * PROSITE sequence motifs
+ * low-complexity regions
+ * nuclear localisation signals
+ * regions lacking regular structure (NORS)
+ * transmembrane helices
+ * transmembrane beta barrels
+ * coiled-coil regions
+ * disulfide-bonds
+ * disordered regions
+ * B-value flexibility
+ * protein-protein interaction sites
Modified: trunk/packages/rostlab/predictprotein/trunk/debian/copyright
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/copyright 2012-07-12 10:13:16 UTC (rev 11753)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/copyright 2012-07-12 10:21:22 UTC (rev 11754)
@@ -1,131 +1,31 @@
-This package was debianized by Guy Yachdav <gyachdav at rostlab.org> on
-Tue, 08 Jun 2010 22:46:33 +0200.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: predictprotein
+Upstream-Contact: Guy Yachdav <gyachdav at rostlab.org>
+Source: ftp://rostlab.org/predictprotein/
-Authors:
+Files: debian/*
+Copyright: 2010 Guy Yachdav <gyachdav at rostlab.org>
+ 2012 Laszlo Kajan <lkajan at rostlab.org>
+ 2012 Simon Domke <domkes at in.tum.de>
+License: GPL-3+
- Burkhard Rost <rost at in.tum.de>
- Antoine De Daruvar <antoine.daruvar at pmtg.u-bordeaux2.fr>
- Jinfeng Liu <jinfeng.liu at gmail.com>
- Guy Yachdav <gyachdav at rostlab.org>
- Laszlo Kajan <lkajan at rostlab.org>
- Markus Schmidberger <schmidberger at rostlab.org>
+Files: *
+Copyright: 2010 ROSTLAB
+License: GPL-3+
-Copyright:
-
- Copyright (C) 2010 ROSTLAB
-
-License:
-
- ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF PredictProtein
-
- By downloading the Software you are consenting to be bound by and become a party to this agreement as the "Licensee". If you do not agree to all of the terms of this agreement, you must not download the software, not install the product nor use the product, and you do not become a LICENSEE under this agreement.
-
- If you are not a member of a publicly funded Academic and/or Education and/or Research Institution you must obtain a commercial license, please send mail to (info at bio-sof.com). This software license agreement is entered into by and between the ROSTLAB, Technical University of Munich (hereinafter "TUM") and the "LICENSEE".
-
- WHEREAS TUM has the right to license all copyrights and other property rights in the Licensed Software identified as PredictProtein and developed by TUM and TUM desires to license the Software so that it becomes available for public use and benefit.
-
- The software is an aggregation of multiple software packages each distributed under its own license (hereinafter sublicenses). Sublicenses terms apply to this license.
-
- WHEREAS LICENSEE is a public funded Academic and/or Education and/or Research Institution.
-
- WHEREAS LICENSEE desires to acquire a free non-exclusive license to use the Software for internal research purposes only.
-
- NOW, THEREFORE, in consideration of the mutual promises and covenants contained herein, the parties agree as follows:
-
- 1. Definitions
-
- "Licensed Software" means the specific version PredictProtein pursuant to this Agreement. Any opinion, findings, conclusions or recommendations expressed in the Licensed Software are those of the authors and do not necessarily reflect the views of TUM.
-
- 2. License
-
- Subject to the terms and conditions of this Agreement a non-exclusive, non-transferable License to use and copy the Licensed Software is made available free of charge for the LICENSEE, which is a non-profit educational, academic, and/or research institution.
-
- The License is only granted for personal and internal use in research only at one Site, where a Site is defined as a set of contiguous buildings in one location. The software will be used at only one location of LICENSEE.
-
- This license does not entitle Licensee to receive from TUM copies of the Licensed software on disks, tapes or CD's, hard-copy documentation, tefghchnical support, telephone assistance, or enhancements or updates to the Licensed Software.
-
- The user and any research assistants, co-workers or other workers who may use the Software agree to not give the program to third parties or grant licenses on software, which include the Software, alone or integrated into other software, to third parties. Modification of the source code is prohibited without the prior written consent of TUM.
-
- 3. Ownership
-
- Except as expressly licensed in this Agreement, The TUM shall retain title to the Licensed Software, and any upgrades and modifications created by TUM.
-
- 4. Consideration
-
- In consideration for the license rights granted by TUM, LICENSEE will obtain this academic license free of charge.
-
- 5. Copies
-
- LICENSEE shall have the right to make copies of the Licensed Software for internal use at the Site and for back-up purposes under this Agreement, but agrees that all such copies shall contain the copyright notices and all other reasonable and appropriate proprietary markings or confidential legends that appear on the Licensed Software provided hereunder.
-
- 6. Support
-
- The TUM shall have no obligation to offer support services to LICENSEE, and nothing contained herein shall be interpreted as to require TUM to provide maintenance, installation services, version updates, debugging, consultation or end-user support of any kind.
-
- 7. Software Protection
-
- LICENSEE acknowledges that the Licensed Software is proprietary to the TUM. The software code shall be treated as trade secrets and confidential information of TUM, and LICENSEE agrees to use best efforts to hold the same in confidence. LICENSEE's obligation for confidentiality shall not extend to any information which is or becomes generally available to the public, is already known to or subsequently disclosed by third parties to LICENSEE and at its free disposal, or is independently developed by LICENSEE or its affiliates without the use of the confidential information disclosed by TUM, or is required by law or legal process.
-
- Except as otherwise expressly permitted in this Agreement, or expressly permitted by the agreements of the sub-licenses, Licensee my not
-
- (i) redistribute, encumber, sell, rent, lease, sublicense, or otherwise transfer rights to the Licensed Software;
-
- (ii) remove or alter any trademark, logo, copyright or other proprietary notices, legends, symbols or labels in the Product; or
-
- If you want to assess our method to publish results on a new data set, we urge you to communicate this plan with us to ascertain that you are optimally running the software.
-
- 8. Representations of TUM to LICENSEE
-
- TUM represents to LICENSEE that
-
- (i) TUM has the right to grant the License and to enter into this agreement,
-
- (ii) that, to the best of TUM's knowledge, the Licensed software does not infringe any patent, copyright or trade secrets of any third party, provided however that such representation and warranty shall not apply to any addition to, or modifications or adaptation of, the Licensed Software made by LICENSEE
-
- and
-
- (iii) TUM undertakes to use best efforts to cooperate with and assist LICENSEE, at LICENSEE's expense, in defending itself against any action based on the alleged infringement of any third party patent, copyright or trade secret rights resulting from or relating to the use or licensing of the Licensed Software by LICENSEE.
-
- 9. Indemnity and Disclaimer of Warranties
-
- Except as expressly set forth in this agreement, TUM makes no
- representations or warranties, express or implied.
-
- The product is provided free of charge, and, therefore, on an "as is" basis, without warranty of any kind, express or implied, including without limitation the warranties that it is free of defects, virus free, able to operate on an uninterrupted basis, merchantable, fit for a particular purpose or non-interfering. The entire risk as to the quality and performance of the Licensed Software is borne by LICENSEE.
-
- By way of example, but not limitation, TUM makes no representations or warranties of merchantability or fitness for any particular application or, except as set forth in paragraph 8, that the use of the Software will not infringe any patents, copyrights or trademarks or other rights of third parties. The entire risk as to the quality and performance of the product is borne by LICENSEE. TUM shall not be liable for any liability or damages with respect to any claim by LICENSEE or any third party on account of, or arising from the license or use of the Software.
-
- Should the Licensed Software prove defective in any respect, LICENSEE and not LICENSOR or it's affiliates should assume the entire cost of any service and repair. This disclaimer of warranty constitutes an essential part of this agreement. No use of the licensed product is authorized hereunder except under this disclaimer.
-
- In no event will LICENSOR or its affiliates be liable for any indirect, special, incidental or consequential damages arising out of the use of or inability to use the product, 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 advised of the possibility thereof, and regardless of the legal or equitable theory (contract, tort or otherwise) upon which the claim is based.
-
- 10. Promotional Advertising & References
-
- LICENSEE may not use the name of the Licensed Software in its promotional advertising, product literature, and other similar promotional materials to be disseminated to the public or any portion thereof. LICENSEE agrees not to identify TUM in any promotional advertising or other promotional materials to be disseminated to the public, or any portion thereof without TUM's prior written consent.
-
- LICENSEE agrees that any reference to the software will cite one or more publications as set forth in the manual and in agreement with common scientific practice.TUM shall not use LICENSEE's name in publicity or advertising involving this Agreement or otherwise without LICENSEE's prior written consent which may be
- withheld at LICENSEE's sole discretion.
-
- 11. Term
-
- This Agreement and the license rights granted herein shall become effective as of the date this Agreement is executed by both parties and shall be perpetual unless terminated in accordance with this Section.
-
- TUM may terminate this Agreement at any time.
-
- Either party may terminate this Agreement at any time effective upon the other party's breach of any agreement, covenant, or representation made in this Agreement, such breach remaining uncorrected sixty (60) days after written notice thereof. LICENSEE shall have the right, at any time, to terminate this Agreement without cause by written notice to TUM specifying the date of termination.
-
- Upon termination, LICENSEE shall destroy all full and partial copies of the Licensed Software.
-
- 12. Governing Law
-
- This Agreement shall be construed in accordance with the laws of Germany and the state of Bavaria.
-
- 13. General
-
- The parties agree that this Agreement is the complete and exclusive agreement among the parties and supersedes all proposals and prior agreements whether written or oral, and all other communications among the parties relating to the subject matter of this Agreement. This Agreement cannot be modified except in writing and signed by both parties. Failure by either party at any time to enforce any of the provisions of this Agreement shall not constitute a waiver by such party of such provision nor in any way affect the validity of this Agreement.
-
- The invalidity of singular provisions does not affect the validity of the entire understanding. The parties are obligated, however, to replace the invalid provisions by a regulation which comes closest to the economic intent of the invalid provision. The same shall apply mutatis mutandis in case of a gap.
-
- IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be duly executed on the date of the download of the software and by accepting the license conditions by pressing the Acceptance button.
-
-The Debian packaging is (C) 2010, Guy Yachdav <gyachdav at rostlab.org>.
+License: GPL-3+
+ This program 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 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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 program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Copied: trunk/packages/rostlab/predictprotein/trunk/debian/upstream (from rev 11751, trunk/packages/predictprotein/trunk/debian/upstream)
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/upstream (rev 0)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/upstream 2012-07-12 10:21:22 UTC (rev 11754)
@@ -0,0 +1,14 @@
+Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=predictprotein&component=predictprotein&resolution=---
+Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=predictprotein
+Reference:
+ Author: Burkhrd Rost and Guy Yachdav and Jinfeng Liu
+ Title: The PredictProtein server
+ Journal: Nucleic Acids Research
+ Year: 2004
+ Volume: 32
+ Number: 2
+ Pages: W321-W326
+ DOI: 10.1093/nar/gkh377
+ PMID: 15215403
+ URL: http://nar.oxfordjournals.org/content/32/suppl_2/W321.abstract
+ eprint: http://nar.oxfordjournals.org/content/32/suppl_2/W321.full
Modified: trunk/packages/rostlab/predictprotein/trunk/debian/watch
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/watch 2012-07-12 10:13:16 UTC (rev 11753)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/watch 2012-07-12 10:21:22 UTC (rev 11754)
@@ -1,2 +1,2 @@
version=3
-opts=pasv ftp://rostlab.org/predictprotein/predictprotein-([0-9.]+)\.tar\.gz
+opts=pasv ftp://rostlab.org/predictprotein/predictprotein-([0-9.]+)\.tar\.gz debian uupdate
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