debian/0000755000000000000000000000000012221640724007166 5ustar debian/source/0000755000000000000000000000000012143214723010465 5ustar debian/source/format0000644000000000000000000000001412143214311011664 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212157032501010360 0ustar 9 debian/Description0000644000000000000000000000155212216601124011372 0ustar FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011). FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible. A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input. jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example. debian/control0000644000000000000000000000137112221640477010600 0ustar Source: libfreecontact-perl Section: perl Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan Build-Depends: debhelper (>= 9.0.0), libextutils-xspp-perl, libfreecontact0-dev (>= 1.0.21-1~), perl Standards-Version: 3.9.4 Homepage: http://rostlab.org/ Vcs-Git: git://anonscm.debian.org/debian-med/libfreecontact-perl.git Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libfreecontact-perl.git Package: libfreecontact-perl Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, libfreecontact0 (>= 1.0.16-1~) Description: fast protein contact predictor - binding for Perl ${Description} . This package contains the Perl binding. debian/docs0000644000000000000000000000000712143220202010022 0ustar README debian/examples0000644000000000000000000000001712143220222010713 0ustar examples/*.aln debian/watch0000644000000000000000000000021212143220356010210 0ustar # Compulsory line, this is a version 3 file version=3 opts=passive \ ftp://rostlab.org/free/FreeContact-([0-9.]+)\.tar\.gz debian uupdate debian/copyright0000644000000000000000000000214312171550215011120 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: libfreecontact-perl Upstream-Contact: Laszlo Kajan Source: ftp://rostlab.org/free/ Files: debian/* Copyright: 2013 Laszlo Kajan , Technical University of Munich, Germany License: GPL-1+ or Artistic Files: * Copyright: 2012 Laszlo Kajan , Technical University of Munich, Germany License: GPL-1+ or Artistic License: GPL-1+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version. . On Debian systems, the complete text of version 1 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-1'. License: Artistic This program is free software; you can redistribute it and/or modify it under the terms of the Artistic License, which comes with Perl. . On Debian systems, the complete text of the Artistic License can be found in `/usr/share/common-licenses/Artistic'. debian/rules0000755000000000000000000000152512216606735010261 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) Description := $(shell sed -e ':a; N; s/\n/$${Newline}/; ta' < debian/Description) .PHONY: override_dh_auto_configure override_dh_auto_configure: dh_auto_configure -- OPTIMIZE="$(CPPFLAGS) $(CFLAGS)" LD="$(shell perl -V::ld:) $(LDFLAGS)" .PHONY: override_dh_gencontrol override_dh_gencontrol: dh_gencontrol -- '-VDescription=$(Description)' .PHONY: get-orig-source get-orig-source: uscan --verbose --force-download --destdir=.. .PHONY: override_dh_auto_clean override_dh_auto_clean: rm -f Makefile.old dh_auto_clean %: dh $@ --parallel debian/changelog0000644000000000000000000000057312221640674011051 0ustar libfreecontact-perl (0.08-2) unstable; urgency=low * Updated build dependency to new version of libfreecontact0-dev that fixes #724257. -- Laszlo Kajan Sat, 28 Sep 2013 22:51:20 +0200 libfreecontact-perl (0.08-1) unstable; urgency=low * Initial release (Closes: #723747). -- Laszlo Kajan Thu, 19 Sep 2013 15:46:28 +0200 debian/upstream0000644000000000000000000000050012171553615010752 0ustar Name: libfreecontact-perl Contact: Laszlo Kajan Homepage: http://rostlab.org/ Reference: - Author: László Kaján and Thomas A. Hopf and Matúš Kalaš and Debora S. Marks and Burkhard Rost Title: 'FreeContact: ...' Journal: BMC Bioinformatics Year: '201?' # vim:et:ts=2:ai:syntax=yaml: