[med-svn] r11698 - in trunk/packages/predictprotein/trunk: . debian debian/po
Simon Domke
sdomke-guest at alioth.debian.org
Tue Jul 10 14:25:00 UTC 2012
Author: sdomke-guest
Date: 2012-07-10 14:24:59 +0000 (Tue, 10 Jul 2012)
New Revision: 11698
Added:
trunk/packages/predictprotein/trunk/debian/
trunk/packages/predictprotein/trunk/debian/changelog
trunk/packages/predictprotein/trunk/debian/compat
trunk/packages/predictprotein/trunk/debian/control
trunk/packages/predictprotein/trunk/debian/copyright
trunk/packages/predictprotein/trunk/debian/lintian-overrides
trunk/packages/predictprotein/trunk/debian/po/
trunk/packages/predictprotein/trunk/debian/po/POTFILES.in
trunk/packages/predictprotein/trunk/debian/preinst
trunk/packages/predictprotein/trunk/debian/rules
trunk/packages/predictprotein/trunk/debian/svn-commit.tmp
trunk/packages/predictprotein/trunk/debian/templates
Log:
Added: trunk/packages/predictprotein/trunk/debian/changelog
===================================================================
--- trunk/packages/predictprotein/trunk/debian/changelog (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/changelog 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,533 @@
+predictprotein (1.0.79) UNRELEASED; urgency=low
+
+ * reprof integration moved to its own branch while experimental
+ * metadisorder a Suggests: because it is non-redistributable for all.
+ * Removing disis Suggests per Burkhard's request: we do not trust the
+ method any more, Yanay had some funny results with the packaged version.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 02 Jul 2012 16:10:40 +0200
+
+predictprotein (1.0.78) unstable; urgency=low
+
+ * Added --print-ext-method-map cmd line argument.
+ * Removed unnecessary libnhgri-blastall-perl dependency.
+ * profcon is no longer a dependency of any sort.
+ * hmm3pfam is now a default target. Promoted Suggests: of hmmer to Depends:.
+ * disis back to Suggests and an optional target because of svm-light5 dependency that can not make it into Debian (non-redistributable).
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 19 Jun 2012 11:24:31 +0200
+
+predictprotein (1.0.77) unstable; urgency=low
+
+ * [Laszlo Kajan <lkajan at rostlab.org>]
+ Demoting pp-cache-mgr dependency to Suggests - as this pack is not
+ necessary for the default configuration and should not be pulled in
+ automatically because of 'Recommends'.
+
+ * [Guy Yachdav <gyachdav at rostlab.org>]
+ Added reprof in alpha mode
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Mon, 4 Jun 2012 21:03:15 +0200
+
+predictprotein (1.0.76) unstable; urgency=low
+
+ * Depends on profdisis
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 21 Feb 2012 14:06:07 +0100
+
+predictprotein (1.0.75) unstable; urgency=low
+
+ * profdisis target now in 'all' as svm-light5 is now redistributable by us
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 21 Feb 2012 13:29:31 +0100
+
+predictprotein (1.0.74) unstable; urgency=low
+
+ * fixed proftmb Makefile rule bug
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 17 Feb 2012 17:12:45 +0100
+
+predictprotein (1.0.73) unstable; urgency=low
+
+ * Reconfigure to work with HHomp-compatible (newer) proftmb.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 17 Feb 2012 16:03:47 +0100
+
+predictprotein (1.0.72) unstable; urgency=low
+
+ * Changed section to non-free/science.
+ * Updated manpage.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 17 Dec 2011 02:27:11 +0100
+
+predictprotein (1.0.71) unstable; urgency=low
+
+ * output dir for examples now /tmp/pp
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 15 Dec 2011 22:10:11 +0100
+
+predictprotein (1.0.70) unstable; urgency=low
+
+ * removed profchop dependency as we never actually called it
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 15 Dec 2011 22:09:07 +0100
+
+predictprotein (1.0.69) unstable; urgency=low
+
+ * hmm3pfam moved to be an optional target because Bio-Linux dependencies
+ can not handle the upgrade to version 3 of it
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 15 Dec 2011 21:47:21 +0100
+
+predictprotein (1.0.68) unstable; urgency=low
+
+ * conflicts with coiledcoils
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 27 Oct 2011 20:24:16 +0200
+
+predictprotein (1.0.67) unstable; urgency=low
+
+ * dep now on ncoils as a replacement of coiledcoils
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 22 Oct 2011 11:18:12 +0200
+
+predictprotein (1.0.66) unstable; urgency=low
+
+ * the error.log generated by occational blast in psic is now handled
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 21 Oct 2011 13:12:47 +0200
+
+predictprotein (1.0.65) unstable; urgency=low
+
+ * --prosite-dat to give loctree the prosite.dat database path
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 21 Oct 2011 12:07:18 +0200
+
+predictprotein (1.0.64) unstable; urgency=low
+
+ * exposed new loctree cmd line arg for Swiss-Prot keyword-to-accession
+ 'index'
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 18 Oct 2011 16:58:36 +0200
+
+predictprotein (1.0.63) unstable; urgency=low
+
+ * updated cache_merge logic: now no merging occurs when the cache is empty
+ * fixed DESTDIR vulnerability due to lack of quoting in Makefile - DESTDIR
+ now accepts all valid paths
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 19 Sep 2011 17:57:01 +0200
+
+predictprotein (1.0.62) unstable; urgency=low
+
+ * Merging, when --target is used, is now default only when there already
+ is something in the cache.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 19 Sep 2011 17:55:26 +0200
+
+predictprotein (1.0.61) unstable; urgency=low
+
+ * fixed --output-dir bug when it is not a fully qualified path
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 15 Sep 2011 15:44:48 +0200
+
+predictprotein (1.0.60) unstable; urgency=low
+
+ * fixed --target switching on cache merging when nouse-cache is given
+ * added ~/.predictproteinrc to the conf file list
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 28 Jun 2011 17:42:29 +0200
+
+predictprotein (1.0.59) unstable; urgency=low
+
+ * removed >> 8 from $? error reporting in predictprotein
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 03 Jun 2011 14:13:55 +0200
+
+predictprotein (1.0.58) unstable; urgency=low
+
+ * added code to recover STDERR of blast calls and disulfinder in case
+ of failure even if not in debug mode
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 20 May 2011 22:13:21 +0200
+
+predictprotein (1.0.57) unstable; urgency=low
+
+ * fixed exit 255 bug
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 18 May 2011 22:35:50 +0200
+
+predictprotein (1.0.56) unstable; urgency=low
+
+ * more rigorous cleaning up after ppc_lock
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 18 May 2011 14:05:32 +0200
+
+predictprotein (1.0.55) unstable; urgency=low
+
+ * blastall error.log is now automatically removed
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sun, 15 May 2011 20:16:02 +0200
+
+predictprotein (1.0.54) unstable; urgency=low
+
+ * clustalw results from psic are now retained in cache - gzipped
+ * switch make to workdir with -C now - this makes targets like query.asp
+ work
+ * --cache-merge cache merging implemented, this is now ON by default
+ in case use_cache is in effect
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 05 May 2011 21:49:16 +0200
+
+predictprotein (1.0.53) unstable; urgency=low
+
+ * .hssp80 is removed from light_cache list because Esmeralda needs it
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 20 Apr 2011 18:24:11 +0200
+
+predictprotein (1.0.52) unstable; urgency=low
+
+ * Added light_cache config file value to control caching of big and rarely
+ needed files. With light_cache set to 1 .safBlastPsi .safBlastPsi80 .hssp
+ and .hssp80 are not stored into the cache
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 15 Apr 2011 14:17:24 +0200
+
+predictprotein (1.0.51) unstable; urgency=low
+
+ * now uses runNewPSIC.pl from the rost-runpsic package
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 12 Apr 2011 12:33:33 +0200
+
+predictprotein (1.0.50) unstable; urgency=low
+
+ * added --makedebug cmd line argument to trigger --debug of make
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 11 Mar 2011 15:37:14 +0100
+
+predictprotein (1.0.49) unstable; urgency=low
+
+ * proper license presentation in debconf
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 09 Mar 2011 11:41:26 +0100
+
+predictprotein (1.0.48) unstable; urgency=low
+
+ * added debconf check for non-profitness
+ * changed license to academi ala ppmi license
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 09 Mar 2011 10:53:44 +0100
+
+predictprotein (1.0.47) unstable; urgency=low
+
+ * >& now correctly
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 02 Mar 2011 13:08:31 +0100
+
+predictprotein (1.0.46) unstable; urgency=low
+
+ * dash compatible shell syntax
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 02 Mar 2011 10:37:40 +0100
+
+predictprotein (1.0.45) stable; urgency=low
+
+ * message when pp-popcon is not installed
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 28 Feb 2011 17:56:33 +0100
+
+predictprotein (1.0.44) stable; urgency=low
+
+ * pp man page mentions popularity contest
+ * in popularity contest
+ * coils-wrap.pl now uses proper tmp dir
+ * removed prodom but kept cmd line arg for compatibility
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 18 Feb 2011 13:27:52 +0100
+
+predictprotein (1.0.43) stable; urgency=low
+
+ * pp-cache-mgr is only recommended now, not a dep; loctree and tmhmm are suggests
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 27 Jan 2011 23:40:18 +0100
+
+predictprotein (1.0.42) stable; urgency=low
+
+ * added predictnls dependency
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 27 Jan 2011 16:35:13 +0100
+
+predictprotein (1.0.41) stable; urgency=low
+
+ * silenced disulfinder
+ * psic now runs with blastpgp results on big80: .blastPsiOutTmp
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 21 Jan 2011 16:32:52 +0100
+
+predictprotein (1.0.40) stable; urgency=low
+
+ * psicexe default changed to /usr/share/librg-utils-perl/runNewPSIC.pl
+ * no more snapfun dependency
+ * added 'make', 'perl' dependency
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 19 Jan 2011 17:12:42 +0100
+
+predictprotein (1.0.39) stable; urgency=low
+
+ * --cpu 4 corrected on hmmscan
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 17 Jan 2011 23:36:54 +0100
+
+predictprotein (1.0.38) stable; urgency=low
+
+ * made loctree recommended 'cause it depends on the non-redistributable
+ SignalP
+ * extended debian/control with paragraphs about tmhmm and loctree
+ * took tmhmm and loctree out of the default target all:, these are now
+ in the optional: target
+ * new config file option: default_targets to control targets made
+ when none is given on the cmd line
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 17 Jan 2011 17:58:02 +0100
+
+predictprotein (1.0.37) stable; urgency=low
+
+ * made tmhmm a suggested package and not a dependency
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Sun, 16 Jan 2011 16:59:06 +0100
+
+predictprotein (1.0.36) stable; urgency=low
+
+ * tidied up MakefilePP.mk: changed references to profnors to norsp
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 04 Jan 2011 11:08:05 +0100
+
+predictprotein (1.0.35) stable; urgency=low
+
+ * switched from included norsp scripts to independent package
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Thu, 23 Dec 2010 15:35:21 +0100
+
+predictprotein (1.0.34) stable; urgency=low
+
+ * norsnet now on disorder target
+ * ...
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 14 Dec 2010 15:34:32 +0100
+
+predictprotein (1.0.33) stable; urgency=low
+
+ * all blasts now 2>/dev/null if not debug
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 19 Oct 2010 14:38:04 +0200
+
+predictprotein (1.0.32) stable; urgency=low
+
+ * --numresmax: maximum sequence length allowed
+ I think convert_seq fails for a seq over 19000.
+ Marco's swissprot analysis:
+ TOTAL NUMBER OF SEQUENCES = 12,265,120
+ 0-1000 11,962,876 0.975
+ 1000-2000 261,633 0.021
+ 2000-3000 25,677 0.002
+ 3000-4000 9,944 0
+ 4000-5000 2,735 0
+ 5000-6000 1,060 0
+ 6000-7000 428 0
+ 7000-8000 366 0
+ 8000-9000 164 0
+ 9000-10000 65 0
+ >10000 171 0
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 19 Oct 2010 14:38:04 +0200
+
+predictprotein (1.0.31) stable; urgency=low
+
+ * --profnumresmin: minimum sequence length required by prof. Sequences
+ shorter than this will make predictprotein fail with 254
+ This value is 17 by default, configurable from the cmd line or config
+ file.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 14 Oct 2010 16:43:48 +0200
+
+predictprotein (1.0.30) stable; urgency=low
+
+ * silenced warnings of %.blastpSwissM8 blastall call (e.g.
+ 'Selenocysteine (U) at position 59 replaced by X')
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 14 Oct 2010 09:28:27 +0200
+
+predictprotein (1.0.29) stable; urgency=low
+
+ * MakefilePP now properly defined rules producing multiple targets -
+ now ready for -j >1 runs
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 13 Oct 2010 18:39:59 +0200
+
+predictprotein (1.0.28) stable; urgency=low
+
+ * psic call with --quiet
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 12 Oct 2010 17:31:17 +0200
+
+predictprotein (1.0.27) stable; urgency=low
+
+ * added configuration options for pfam databases
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 11 Oct 2010 14:17:13 +0200
+
+predictprotein (1.0.26) stable; urgency=low
+
+ * added required version to hmmer dep
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 09 Oct 2010 14:11:34 +0200
+
+predictprotein (1.0.25) stable; urgency=low
+
+ * added missing dependencies
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sat, 09 Oct 2010 14:01:48 +0200
+
+predictprotein (1.0.24) stable; urgency=low
+
+ * fixed tmhmm work dir issue - not current dir but tmp dir now
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 08 Oct 2010 23:31:44 +0200
+
+predictprotein (1.0.23) stable; urgency=low
+
+ * added psic from snap
+ * added loctree with all 3 organism 'types'
+ * added hmmer2 and 3
+ * added prof runs on fasta sequence only (no alignment)
+ * added tmhmm
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 08 Oct 2010 13:59:43 +0200
+
+predictprotein (1.0.22) stable; urgency=low
+
+ * Sequence now converted to upper case before fed into pipeline
+ * Copf now explicitely told to expect FASTA format input file (where
+ appropriate)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 20 Sep 2010 17:13:20 +0200
+
+predictprotein (1.0.21) stable; urgency=low
+
+ * Makefile.am now correctly modifies predictprotein with version number
+ * Debian native now
+ * Unfortunate dependency on discontinued librg-pp-cachemgr-perl removed
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 17 Sep 2010 15:11:28 +0200
+
+predictprotein (1.0.20)
+
+ * Silenced 'wrong parsin htm file??\nctHtm=$ctHtm'
+ * Corrected some grammar issues
+ * Reorganized predictprotein - only for more logical code, no change in what it does
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 16 Aug 2010 21:25:17 +0200
+
+predictprotein (1.0.19)
+
+ * Introduced config file and cmd line params to control: bigblastdb
+ big80blastdb swissblastdb prodomblastdb prositeconvdat
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 16 Aug 2010 19:05:18 +0200
+
+predictprotein (1.0.18)
+
+ * silenced nors.pl
+ * MD make rules according to Avner's original runMD.pl are now included but are not used
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 12 Aug 2010 20:30:57 +0200
+
+predictprotein (1.0.17)
+
+ * file restore logic moved to cache module
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 23 Jul 2010 13:23:00 +0200
+
+predictprotein (1.0.16)
+
+ * redirecting standard output of make of methods to /dev/null if not --debug
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 23 Jul 2010 13:23:00 +0200
+
+predictprotein (1.0.15)
+
+ * fixed filter_blastp_big.pl e-179 error
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 23 Jul 2010 13:23:00 +0200
+
+predictprotein (1.0.14)
+
+ * fixed syntax error
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 23 Jul 2010 13:23:00 +0200
+
+predictprotein (1.0.13)
+
+ * Another example on man page
+ * predictprotein works with cache now
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 23 Jul 2010 13:23:00 +0200
+
+predictprotein (1.0.12)
+
+ * New examples
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 22 Jul 2010 09:35:05 +0200
+
+predictprotein (1.0.11)
+
+ * filter_blastp_big.pl -> helper apps
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 21 Jul 2010 21:53:30 +0200
+
+predictprotein (1.0.10)
+
+ * Helper apps now installed as scripts
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 21 Jul 2010 21:53:30 +0200
+
+predictprotein (1.0.9)
+
+ * predictnls params now correctly given (were paths for fileSummary and fileTrace, boolean is expected)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 21 Jul 2010 21:53:30 +0200
+
+predictprotein (1.0.8)
+
+ * Man pages
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 21 Jul 2010 21:53:30 +0200
+
+predictprotein (1.0.7)
+
+ * System now compatible with cmd line interface of the cache manager and queue manager
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 21 Jul 2010 21:53:30 +0200
+
+predictprotein (1.0.6)
+
+ * Paths for prof, proftmb are now resolved through the config file
+ * Added more version information about the package
+ * Man page had an incorrect example
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Sun, 18 Jul 2010 12:56:19 +0200
+
+predictprotein (1.0.1)
+
+ * Bug Fixes
+ * No longer relies on RG:PP
+ * Runs profdisis
+ * Creates files into output folder and not one concatenated file
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Sat, 17 Jul 2010 14:37:05 +0200
+
+predictprotein (1.0.0)
+
+ * Initial packaged version
+
+ -- Guy Yachdav <gyachdav at rostlab.org> Wed, 28 Apr 2010 15:33:11 +0200
Added: trunk/packages/predictprotein/trunk/debian/compat
===================================================================
--- trunk/packages/predictprotein/trunk/debian/compat (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/compat 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1 @@
+7
Added: trunk/packages/predictprotein/trunk/debian/control
===================================================================
--- trunk/packages/predictprotein/trunk/debian/control (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/control 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,36 @@
+Source: predictprotein
+Section: non-free/science
+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
+Homepage: http://www.predictprotein.org
+
+Package: predictprotein
+Architecture: all
+Conflicts: coiledcoils
+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), lowcompseg, make, norsnet, norsp, perl, predictnls, profbval (>= 1.0.15), profisis, profphd, proftmb (>= 1.1.9-1)
+Recommends: pp-popularity-contest
+Suggests: loctree (>= 1.0.20), metadisorder, pp-cache-mgr (>= 1.0.3), profasp, rost-runpsic (>= 1.0.5), tmhmm (>= 2.0)
+Description: A suite of 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, globular regions, 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.
+ .
+ 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.
Added: trunk/packages/predictprotein/trunk/debian/copyright
===================================================================
--- trunk/packages/predictprotein/trunk/debian/copyright (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/copyright 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,131 @@
+This package was debianized by Guy Yachdav <gyachdav at rostlab.org> on
+Tue, 08 Jun 2010 22:46:33 +0200.
+
+Authors:
+
+ 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>
+
+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>.
Added: trunk/packages/predictprotein/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/predictprotein/trunk/debian/lintian-overrides (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/lintian-overrides 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1 @@
+predictprotein: using-first-person-in-templates shared/predictprotein/academic
Added: trunk/packages/predictprotein/trunk/debian/po/POTFILES.in
===================================================================
--- trunk/packages/predictprotein/trunk/debian/po/POTFILES.in (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/po/POTFILES.in 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1 @@
+[type: gettext/rfc822deb] templates
Added: trunk/packages/predictprotein/trunk/debian/preinst
===================================================================
--- trunk/packages/predictprotein/trunk/debian/preinst (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/preinst 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,90 @@
+#!/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:
Property changes on: trunk/packages/predictprotein/trunk/debian/preinst
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/predictprotein/trunk/debian/rules
===================================================================
--- trunk/packages/predictprotein/trunk/debian/rules (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/rules 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,107 @@
+#!/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
+
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+ifneq ($(DEB_HOST_GNU_TYPE),$(DEB_BUILD_GNU_TYPE))
+CROSS= --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE)
+else
+CROSS= --build $(DEB_BUILD_GNU_TYPE)
+endif
+
+
+
+config.status: configure
+ dh_testdir
+ # Add here commands to configure the package.
+ifneq "$(wildcard /usr/share/misc/config.sub)" ""
+ cp -f /usr/share/misc/config.sub config.sub
+endif
+ifneq "$(wildcard /usr/share/misc/config.guess)" ""
+ cp -f /usr/share/misc/config.guess config.guess
+endif
+ ./configure $(CROSS) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs" --sysconfdir=/etc
+
+
+build: build-stamp
+
+build-stamp: config.status
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ #docbook-to-man debian/predictprotein.sgml > predictprotein.1
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ [ ! -f Makefile ] || $(MAKE) distclean
+ rm -f config.sub config.guess
+
+ dh_clean
+ debconf-updatepo
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/predictprotein.
+ $(MAKE) DESTDIR=$(CURDIR)/debian/predictprotein install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ dh_lintian
+ dh_installexamples
+# dh_install
+# dh_installmenu
+ dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_python
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture-dependent files here.
+binary-arch: build install
+# We have nothing to do by default.
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/predictprotein/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/predictprotein/trunk/debian/svn-commit.tmp
===================================================================
--- trunk/packages/predictprotein/trunk/debian/svn-commit.tmp (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/svn-commit.tmp 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,4 @@
+
+-- Diese und die folgenden Zeilen werden ignoriert --
+
+A svn+ssh://sdomke-guest@svn.debian.org/svn/debian-med/trunk/packages/predictprotein/trunk
Added: trunk/packages/predictprotein/trunk/debian/templates
===================================================================
--- trunk/packages/predictprotein/trunk/debian/templates (rev 0)
+++ trunk/packages/predictprotein/trunk/debian/templates 2012-07-10 14:24:59 UTC (rev 11698)
@@ -0,0 +1,120 @@
+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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