debian/0000755000000000000000000000000012034602233007161 5ustar debian/README.Debian0000644000000000000000000000026311640373775011245 0ustar profphd-utils for Debian ------------------------ This package presents the binary utilities for profphd. -- Laszlo Kajan Fri, 18 Dec 2009 23:42:34 +0100 debian/watch0000644000000000000000000000011311664744242010224 0ustar version=3 ftp://rostlab.org/profphd-utils/profphd-utils-([0-9.]+)\.tar\.gz debian/rules0000755000000000000000000000065012034601633010245 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export FFLAGS:=$(shell dpkg-buildflags --get FFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) export prefix=/usr %: dh $@ --parallel .PHONY: build install get-orig-source get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/changelog0000644000000000000000000000330712012402000011020 0ustar profphd-utils (1.0.10-1) unstable; urgency=low * New upstream release. -- Laszlo Kajan Tue, 14 Aug 2012 09:29:31 +0200 profphd-utils (1.0.9-1) unstable; urgency=low * New upstream release. * Changed from cdbs to dh. -- Laszlo Kajan Fri, 01 Jun 2012 12:56:21 +0200 profphd-utils (1.0.8-1) unstable; urgency=low * Initial release in Debian (Closes: #643323) -- Laszlo Kajan Tue, 27 Sep 2011 10:08:18 +0200 profphd-utils (1.0.6) unstable; urgency=low * Debian native now -- Laszlo Kajan Mon, 28 Feb 2011 15:50:38 +0100 profphd-utils (1.0.5) * Introduced AM_FFLAGS; FFLAGS now can be used on the command line/ENV as expected -- Laszlo Kajan Thu, 01 Apr 2010 11:53:35 +0200 profphd-utils (1.0.4) * increased MAXCORE to 16777216 in filter_hssp.f in order to allow a big alignment to fit (DMD_HUMAN.hssp example) * Made sequence names case sensitive for READ_MSF routine - solves bug with 3h4p_A and 3h4p_a chains mistaken for the same thing -- Laszlo Kajan Tue, 12 Jan 2010 12:17:03 +0100 profphd-utils (1.0.3) * Removed unnecessary directories; made not to install *.{LINUX,ALPHA,etc} files * lib-sys-linux.f was duplicate of lib-sys-LINUX.f - lib-sys-linux.f removed * Distribute only .LINUX version of lib-sys-*.f -- Laszlo Kajan Tue, 05 Jan 2010 23:18:07 +0100 profphd-utils (1.0.2) * Fixed uninitialized variables without -flocal-init-zero -- Laszlo Kajan Tue, 05 Jan 2010 23:18:07 +0100 profphd-utils (1.0.1) * Initial version -- Laszlo Kajan Fri, 18 Dec 2009 23:23:21 +0100 debian/control0000644000000000000000000000157111762153324010601 0ustar Source: profphd-utils Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan Build-Depends: debhelper (>= 7.0.50~), gfortran Standards-Version: 3.9.3 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/profphd-utils/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/profphd-utils/trunk/ DM-Upload-Allowed: yes Homepage: http://www.rostlab.org/ Package: profphd-utils Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: profphd Description: profphd helper utilities convert_seq and filter_hssp The package provides the following binary utilities: convert_seq, filter_hssp. These are used by prof from the profphd package: a secondary structure, accessibility and transmembrane helix predictor from Burkhard Rost. debian/compat0000644000000000000000000000000211640373775010401 0ustar 7 debian/README.source0000644000000000000000000000073712034602221011344 0ustar profphd-utils for Debian ======================== lintian warnings ---------------- W: profphd-utils: hardening-no-fortify-functions usr/bin/convert_seq W: profphd-utils: hardening-no-fortify-functions usr/bin/filter_hssp These binaries are compiled from gfortran source only. As far as I can tell, all the flags are set. blhc(1) does not report problems. I think these are false positives, but I do not want to override the warning, in order maintain awareness of this issue. debian/copyright0000644000000000000000000000400311640373775011133 0ustar This package was debianized by Laszlo Kajan on Fri, 18 Dec 2009 23:42:34 +0100. It was downloaded from: ftp://rostlab.org/profphd-utils/ Upstream Authors: Reinhard Schneider Ulrike Goebel C. Sander Burkhard Rost Bug fixes and enhancements by: Laszlo Kajan and Guy Yachdav Copyright: Copyright 1998-2011 by Burkhard Rost EMBL, CUBIC (Columbia University, NY, USA) and LION Biosciences (Heidelberg, DE) Copyright 1994 by C. Sander MPIMF (Heidelberg, DE) Copyright 2009-2011 by Guy Yachdav CUBIC (Columbia University, NY, USA), Technical University Munich (Munich, DE), Biosof LLC (USA) Copyright 2009-2011 by Laszlo Kajan Technical University Munich (Munich, DE) Copyright 1988,1991,1997 by Reinhard Schneider LION Biosciences (Heidelberg, DE) Copyright 1997 by Ulrike Goebel LION Biosciences (Heidelberg, DE) License: This package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. The Debian packaging is: (C) 2009, Laszlo Kajan and is licensed under the GPL, see above. debian/patches/0000755000000000000000000000000012034602232010607 5ustar debian/source/0000755000000000000000000000000012034602232010460 5ustar debian/source/format0000644000000000000000000000001411640373775011711 0ustar 3.0 (quilt)