[med-svn] r11742 - trunk/packages/rostlab/predictprotein/trunk/debian
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed Jul 11 15:31:52 UTC 2012
Author: lkajan-guest
Date: 2012-07-11 15:31:52 +0000 (Wed, 11 Jul 2012)
New Revision: 11742
Removed:
trunk/packages/rostlab/predictprotein/trunk/debian/lintian-overrides
trunk/packages/rostlab/predictprotein/trunk/debian/po/
trunk/packages/rostlab/predictprotein/trunk/debian/preinst
trunk/packages/rostlab/predictprotein/trunk/debian/templates
Modified:
trunk/packages/rostlab/predictprotein/trunk/debian/compat
trunk/packages/rostlab/predictprotein/trunk/debian/control
Log:
removed debconf related files no longer necessary because of new license
Modified: trunk/packages/rostlab/predictprotein/trunk/debian/compat
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/compat 2012-07-11 15:27:58 UTC (rev 11741)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/compat 2012-07-11 15:31:52 UTC (rev 11742)
@@ -1 +1 @@
-7
+8
Modified: trunk/packages/rostlab/predictprotein/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/control 2012-07-11 15:27:58 UTC (rev 11741)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/control 2012-07-11 15:31:52 UTC (rev 11742)
@@ -3,8 +3,8 @@
Priority: extra
Maintainer: Guy Yachdav <gyachdav at rostlab.org>
Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 7), autotools-dev, po-debconf
-Standards-Version: 3.9.1
+Build-Depends: debhelper (>= 8), autotools-dev, po-debconf
+Standards-Version: 3.9.3
Homepage: http://www.predictprotein.org
Package: predictprotein
@@ -13,7 +13,7 @@
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)
Recommends: pp-popularity-contest
Suggests: pp-cache-mgr (>= 1.0.3), predictprotein-nonfree
-Description: suite of sequence analysis tools
+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
@@ -25,11 +25,3 @@
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.
- .
- tmhmm (http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm) is non-
- redistributable. Please obtain your own version and configure
- predictprotein accordingly.
- .
- loctree depends on SignalP (http://www.cbs.dtu.dk/services/SignalP/) that
- is non-redistributable. Please obtain your own version and configure
- predictprotein accordingly.
Deleted: trunk/packages/rostlab/predictprotein/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/lintian-overrides 2012-07-11 15:27:58 UTC (rev 11741)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/lintian-overrides 2012-07-11 15:31:52 UTC (rev 11742)
@@ -1 +0,0 @@
-predictprotein: using-first-person-in-templates shared/predictprotein/academic
Deleted: trunk/packages/rostlab/predictprotein/trunk/debian/preinst
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/preinst 2012-07-11 15:27:58 UTC (rev 11741)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/preinst 2012-07-11 15:31:52 UTC (rev 11742)
@@ -1,90 +0,0 @@
-#!/bin/sh
-# preinst script for #PACKAGE#
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# do we have debconf?
-if [ -f /usr/share/debconf/confmodule ]; then
- . /usr/share/debconf/confmodule
- DEBCONF=true
-else
- DEBCONF=
-fi
-
-
-# summary of how this script can be called:
-# * <new-preinst> `install'
-# * <new-preinst> `install' <old-version>
-# * <new-preinst> `upgrade' <old-version>
-# * <old-preinst> `abort-upgrade' <new-version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-validate_academic() {
- if [ -n "$DEBCONF" ]; then
- db_input high shared/predictprotein/academic || true
- db_go || true
-
- # Throw error if not academic or equivalent:
- db_get shared/predictprotein/academic
- if [ "$RET" != "true" ]; then
- # The user is for profit - $$$ - but perhaps this system should forget about it so that the question is asked again.
- #db_unregister shared/predictprotein/academic
-
- #db_fset shared/predictprotein/contact_biosof seen false
- db_input high shared/predictprotein/contact_biosof || true
- db_go || true
- db_purge || true
- echo "aborting - ineligible organization" >&2;
- exit 1;
- fi
- else
- # no debconf, fall back
- cat << EOF
-This package is provided for non-profit educational, academic, and/or research
-institutions only.
-Organizations not covered under the license and users representing them please
-contact info at bio-sof.com to obtain a commercial license.
-EOF
- echo -n "Do you represent a non-profit educational, academic, and/or research institution? (y/n)" >&2
- read line
- case ${line} in
- y|yes|Y|Yes|YES)
- ;;
-
- *) echo "Please contact info at bio-sof.com to obtain a commercial license." >&2
- echo "This package is provided for non-profit educational, academic, and/or research institutions only. This installation is now going to abort." >&2
- exit 1
- ;;
- esac
- fi
-
-}
-
-case "$1" in
- install)
- validate_academic
- ;;
-
- upgrade)
- ;;
-
- abort-upgrade)
- ;;
-
- *)
- echo "preinst 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
-
-# vim:ai:
Deleted: trunk/packages/rostlab/predictprotein/trunk/debian/templates
===================================================================
--- trunk/packages/rostlab/predictprotein/trunk/debian/templates 2012-07-11 15:27:58 UTC (rev 11741)
+++ trunk/packages/rostlab/predictprotein/trunk/debian/templates 2012-07-11 15:31:52 UTC (rev 11742)
@@ -1,120 +0,0 @@
-Template: shared/predictprotein/academic
-Type: boolean
-Default: false
-_Description: Do you represent a non-profit educational, academic, and/or research institution?
- 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.
-
-Template: shared/predictprotein/contact_biosof
-Type: note
-_Description: Please contact info at bio-sof.com to obtain a commercial license
- This package is provided for non-profit educational, academic, and/or research institutions only. This installation is now going to abort.
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