This is an automated email from the git hooks/post-receive script. lkajan pushed a commit to branch master in repository libfreecontact-perl.
commit 0cf231e8815359f0e1389a709b66866549737741 Author: Laszlo Kajan <[email protected]> Date: Fri May 10 18:37:58 2013 +0200 Debianization first version --- .gitignore | 8 ++++++++ debian/Description | 17 +++++++++++++++++ debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 18 ++++++++++++++++++ debian/copyright | 28 ++++++++++++++++++++++++++++ debian/docs | 1 + debian/examples | 1 + debian/rules | 25 +++++++++++++++++++++++++ debian/source/format | 1 + debian/watch | 4 ++++ 11 files changed, 109 insertions(+) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..95b9ad0 --- /dev/null +++ b/.gitignore @@ -0,0 +1,8 @@ +*.o +Makefile +blib/ +debian/files +debian/libfreecontact-perl.debhelper.log +debian/libfreecontact-perl.substvars +debian/libfreecontact-perl/ +pm_to_blib diff --git a/debian/Description b/debian/Description new file mode 100644 index 0000000..4a4cba2 --- /dev/null +++ b/debian/Description @@ -0,0 +1,17 @@ +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, 10-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. diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..19728d4 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +libfreecontact-perl (0.01-1) UNRELEASED; urgency=low + + * Initial release (Closes: #nnnn) + + -- Laszlo Kajan <[email protected]> Fri, 10 May 2013 17:56:55 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..7f8f011 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +7 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..912c64b --- /dev/null +++ b/debian/control @@ -0,0 +1,18 @@ +Source: libfreecontact-perl +Section: perl +Priority: extra +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Laszlo Kajan <[email protected]> +Build-Depends: debhelper (>= 7.0.50~), libextutils-xspp-perl, perl +Standards-Version: 3.9.4 +Vcs-Git: git://git.debian.org/debian-med/libfreecontact-perl.git +Vcs-Browser: http://git.debian.org/?p=debian-med/libfreecontact-perl.git +Homepage: http://rostlab.org/ + +Package: libfreecontact-perl +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends} +Description: fast protein contact predictor - binding for Perl + ${Description} + . + This package contains the Perl binding. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..f90eb39 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,28 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: libfreecontact-perl +Upstream-Contact: Laszlo Kajan <[email protected]> +Source: http://rostlab.org/ + +Files: debian/* +Copyright: 2013 Laszlo Kajan <[email protected]>, Technical University of Munich, Germany +License: GPL-1+ or Artistic + +Files: * +Copyright: 2012 Laszlo Kajan <[email protected]>, Technical University of Munich, Germany +License: GPL-1+ or Artistic + +License: GPL-1+ + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 1, or (at your option) + any later version. + . + On Debian systems, the complete text of version 1 of the GNU General + Public License can be found in `/usr/share/common-licenses/GPL-1'. + +License: Artistic + This program is free software; you can redistribute it and/or modify + it under the terms of the Artistic License, which comes with Perl. + . + On Debian systems, the complete text of the Artistic License can be + found in `/usr/share/common-licenses/Artistic'. diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..e845566 --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +README diff --git a/debian/examples b/debian/examples new file mode 100644 index 0000000..d4e7101 --- /dev/null +++ b/debian/examples @@ -0,0 +1 @@ +examples/*.aln diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..d8e31ce --- /dev/null +++ b/debian/rules @@ -0,0 +1,25 @@ +#!/usr/bin/make -f +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +export CPPFLAGS:=$(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=.. + +%: + dh --parallel $@ diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..f9384e9 --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +# Compulsory line, this is a version 3 file +version=3 +opts=passive \ +ftp://rostlab.org/free/FreeContact-([0-9.]+)\.tar\.gz debian uupdate -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/libfreecontact-perl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
