debian/0000755000000000000000000000000012012535603007163 5ustar debian/README.Debian0000644000000000000000000000125512010173601011221 0ustar profisis for Debian =================== profisis nags the user that he/she has to install pp-popularity-contest (which already is a Recommends) ------------------------------------------------------------------------------------------------------- This is the explicit intention of upstream. The software being released free, this is upstream's way of keeping usage counts. That in turn is used to decide what to support upstream and what not. Q: How to silence the warning? A1: Install the 'pp-popularity-contest' package. A2: Create an executable (script) named 'pp_popcon_cnt' and put it somewhere on your $PATH. The program does not need to do anything, an 'exit' is enough. debian/source/0000755000000000000000000000000012012535545010470 5ustar debian/source/format0000644000000000000000000000001411776745235011715 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000036511777767145011377 0ustar profisis for Debian =================== Uncompressed examples --------------------- dh_compress excludes examples that appear on the man page. This is in order to allow the example to work as it is pasted on the command like from the man page. debian/copyright0000644000000000000000000000424612010173601011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Yanay Ofran Upstream-Name: profisis Source: ftp://rostlab.org/free/ Files: debian/* Copyright: 2012 Cedric Staniewski 2010, 2012 Laszlo Kajan License: GPL-3.0+ Files: examples/3A1P_A.rdbProf Copyright: Burkhard Rost, CUBIC NYC / LION Heidelberg License: GPL-2.0+ Comment: License is not indicated in this file, only copyright. Therefore the license here is that of the producing program 'profphd'. Files: * Copyright: 2006 Yanay Ofran 2006 Burkhard Rost License: GPL-3.0+ License: GPL-2.0+ 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 2 of the License, or (at your option) any later version. . This package 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 . . 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: GPL-3.0+ 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 package 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 . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/upstream0000644000000000000000000000112611776745235010772 0ustar Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=profisis&component=profisis&resolution=--- Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=profisis Reference: Author: Yanay Ofran and Burkhard Rost Title: "ISIS: interaction sites identified from sequence" Journal: Bioinformatics Year: 2007 Volume: 23 Number: 2 Pages: e13-e16 DOI: 10.1093/bioinformatics/btl303 PMID: 17237081 Type: article URL: http://bioinformatics.oxfordjournals.org/content/23/2/e13.abstract Eprint: http://bioinformatics.oxfordjournals.org/content/23/2/e13.full.pdf+html debian/rules0000755000000000000000000000035011777767145010272 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 .PHONY: override_dh_compress override_dh_compress: dh_compress -Xexamples/3A1P_A.fasta -Xexamples/3A1P_A.hssp -Xexamples/3A1P_A.rdbProf %: dh $@ debian/watch0000644000000000000000000000011411777501464010227 0ustar version=3 ftp://rostlab.org/free/profisis-([0-9.]+)\.tar\.gz debian uupdate debian/changelog0000644000000000000000000000243312012535603011037 0ustar profisis (1.0.11-1) unstable; urgency=low * Initial release (Closes: #680106) [Laszlo Kajan ] * Fixed URL in d/control. * Put a note about pp-popularity-contest (nagging) in d/README.Debian. * Added copyright and license of examples/3A1P_A.rdbProf to d/copyright. -- Cedric Staniewski Mon, 09 Jul 2012 20:22:37 +0200 profisis (1.0.5) stable; urgency=low * warn if pp-popcon is not installed -- Laszlo Kajan Mon, 28 Feb 2011 18:17:50 +0100 profisis (1.0.4) stable; urgency=low * Debian native now * bugzilla url * popularity contest -- Laszlo Kajan Fri, 18 Feb 2011 22:35:59 +0100 profisis (1.0.3) * profrdb -> rdbProf for consistency - second attempt -- Laszlo Kajan Fri, 07 May 2010 14:09:13 +0200 profisis (1.0.2) * Corrected man page environment variable * profrdb -> rdbprof for consistency -- Laszlo Kajan Fri, 07 May 2010 14:09:13 +0200 profisis (1.0.1) * Updated manpage with example and other sections * Examples are now installed -- Laszlo Kajan Sat, 24 Apr 2010 20:30:53 +0200 profisis (1.0.0) * Initial packaged version -- Laszlo Kajan Sat, 24 Apr 2010 20:30:53 +0200 debian/compat0000644000000000000000000000000211776745235010405 0ustar 8 debian/control0000644000000000000000000000166012010173601010563 0ustar Source: profisis Section: science Priority: extra Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Cedric Staniewski Build-Depends: debhelper (>= 8) Standards-Version: 3.9.3 Homepage: https://rostlab.org/owiki/index.php/PROFisis Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/profisis/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/profisis/trunk/ Package: profisis Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, libconfig-inifiles-perl, profnet-isis Recommends: librg-utils-perl, pp-popularity-contest Description: prediction of protein-protein interaction sites from sequence Profisis (ISIS) identifies interacting protein residues in protein-protein interfaces from sequence alone. . The strongest predictions of the method reached over 90% accuracy in a cross-validation experiment.