[med-svn] r804 - in trunk/packages: . vienna-rna vienna-rna/trunk vienna-rna/trunk/debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Wed Nov 14 00:56:08 UTC 2007
Author: smoe-guest
Date: 2007-11-14 00:56:08 +0000 (Wed, 14 Nov 2007)
New Revision: 804
Added:
trunk/packages/vienna-rna/
trunk/packages/vienna-rna/trunk/
trunk/packages/vienna-rna/trunk/debian/
trunk/packages/vienna-rna/trunk/debian/README.Debian
trunk/packages/vienna-rna/trunk/debian/changelog
trunk/packages/vienna-rna/trunk/debian/compat
trunk/packages/vienna-rna/trunk/debian/control
trunk/packages/vienna-rna/trunk/debian/copyright
trunk/packages/vienna-rna/trunk/debian/dirs
trunk/packages/vienna-rna/trunk/debian/docs
trunk/packages/vienna-rna/trunk/debian/menu.ex
trunk/packages/vienna-rna/trunk/debian/rules
trunk/packages/vienna-rna/trunk/debian/vienna-rna-default.ex
trunk/packages/vienna-rna/trunk/debian/vienna-rna.doc-base.EX
trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
trunk/packages/vienna-rna/trunk/debian/watch
Log:
Seed attempt to build the Vienna RNA package, which is much respected
world-wide and ... non-free. I'll do the ITP tomorrow.
Property changes on: trunk/packages/vienna-rna/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/vienna-rna/trunk/debian/README.Debian
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/README.Debian 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,13 @@
+vienna-rna for Debian
+---------------------
+
+The package is non-free, nevertheless, I have interest in it and want
+make my initial packaging attempt available for the community.
+
+I'd be glad if someone could take over.
+
+Cheers,
+
+Steffen
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 14 Nov 2007 00:57:29 +0100
Added: trunk/packages/vienna-rna/trunk/debian/changelog
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/changelog (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/changelog 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,6 @@
+vienna-rna (1.6.5-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 14 Nov 2007 00:57:29 +0100
+
Added: trunk/packages/vienna-rna/trunk/debian/compat
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/compat (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/compat 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1 @@
+5
Added: trunk/packages/vienna-rna/trunk/debian/control
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/control (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/control 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,29 @@
+Source: vienna-rna
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 5), autotools-dev
+Standards-Version: 3.7.2
+Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
+
+Package: vienna-rna
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: RNA sequence analysis
+ The Vienna RNA Package consists of a C code library and several
+ stand-alone programs for the prediction and comparison of RNA secondary
+ structures. It is developed and maintained by the group of Ivo Hofacker
+ in Vienna.
+ .
+ RNA secondary structure prediction through energy minimization is the
+ most used function in the package. We provide three kinds of dynamic
+ programming algorithms for structure prediction: the minimum free energy
+ algorithm of (Zuker & Stiegler 1981) which yields a single optimal
+ structure, the partition function algorithm of (McCaskill 1990) which
+ calculates base pair probabilities in the thermodynamic ensemble, and
+ the suboptimal folding algorithm of (Wuchty et.al 1999) which generates
+ all suboptimal structures within a given energy range of the optimal
+ energy. For secondary structure comparison, the package contains several
+ measures of distance (dissimilarities) using either string alignment or
+ tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm
+ to design sequences with a predefined structure (inverse folding).
Added: trunk/packages/vienna-rna/trunk/debian/copyright
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/copyright (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/copyright 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,39 @@
+This package was debianized by Steffen Moeller <moeller at debian.org> on
+Wed, 14 Nov 2007 00:57:29 +0100.
+
+It was downloaded from http://www.tbi.univie.ac.at/~ivo/RNA/
+
+Upstream Authors:
+
+ Ivo Hofacker (all parts)
+ Peter Stadler (design, documentation, cluster algorithms)
+ Walter Fontana (suboptimal folding, pre-historic implementation of mfe folding)
+ Stefan Wuchty (suboptimal folding)
+ Stephan Bernhart (cofolding, local folding)
+ Ulli Mueckstein (RNAup)
+
+Copyright:
+
+ Ivo Hofacker <rna at tbi.univie.ac.at>
+
+License:
+
+ The programs, library and source code of the Vienna RNA Package are
+ free software. They are distributed in the hope that they will be
+ useful but WITHOUT ANY WARRANTY; without even the implied warranty
+ of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+ Permission is granted for research, educational, and commercial use
+ and modification so long as 1) the package and any derived works are
+ not redistributed for any fee, other than media costs, 2) proper
+ credit is given to the authors and the Institute for Theoretical
+ Chemistry of the University of Vienna.
+
+ If you want to include this software in a commercial product, please
+ contact the authors.
+
+The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/vienna-rna/trunk/debian/dirs
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/dirs (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/dirs 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,2 @@
+usr/bin
+usr/sbin
Added: trunk/packages/vienna-rna/trunk/debian/docs
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/docs (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/docs 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,2 @@
+NEWS
+README
Added: trunk/packages/vienna-rna/trunk/debian/menu.ex
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/menu.ex (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/menu.ex 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,2 @@
+?package(vienna-rna):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
+ title="vienna-rna" command="/usr/bin/vienna-rna"
Added: trunk/packages/vienna-rna/trunk/debian/rules
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/rules (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/rules 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,101 @@
+#!/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 ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+config.status: configure
+ dh_testdir
+ # Add here commands to configure the package.
+ifneq "$(wildcard /usr/share/misc/config.sub)" ""
+ cp -f /usr/share/misc/config.sub config.sub
+endif
+ifneq "$(wildcard /usr/share/misc/config.guess)" ""
+ cp -f /usr/share/misc/config.guess config.guess
+endif
+ ./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
+
+
+build: build-stamp
+
+build-stamp: config.status
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ #docbook-to-man debian/vienna-rna.sgml > vienna-rna.1
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ #$(MAKE) distcleancheck
+ find . -name "*.o" -o -name "*.a" -o -name "*.so" | xargs -r rm
+ rm -f config.sub config.guess
+
+ for d in man Progs Utils; do if [ -r $d/Makefile ]; then $(MAKE) -C $d distclean; fi; done
+
+ dh_clean --exclude ./Readseq/ureadseq.c.orig --exclude ./Readseq/readseq.c.orig --exclude ./Readseq/ureadseq.h.orig
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k --exclude ./Readseq/ureadseq.c.orig --exclude ./Readseq/readseq.c.orig --exclude ./Readseq/ureadseq.h.orig
+ dh_installdirs
+
+ # does not work since attempt to access /usr/Ü directly
+ #$(MAKE) DESTDIR=$(CURDIR)/debian/vienna-rna install
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs ChangeLog
+ dh_installdocs
+ 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 man/*.{1,3} RNAforester/man/*.{1,3} Cluster/*.{1,3}
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/vienna-rna/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/vienna-rna/trunk/debian/vienna-rna-default.ex
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna-default.ex (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna-default.ex 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,10 @@
+# Defaults for vienna-rna initscript
+# sourced by /etc/init.d/vienna-rna
+# installed at /etc/default/vienna-rna by the maintainer scripts
+
+#
+# This is a POSIX shell fragment
+#
+
+# Additional options that are passed to the Daemon.
+DAEMON_OPTS=""
Added: trunk/packages/vienna-rna/trunk/debian/vienna-rna.doc-base.EX
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.doc-base.EX (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.doc-base.EX 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,22 @@
+Document: vienna-rna
+Title: Debian vienna-rna Manual
+Author: <insert document author here>
+Abstract: This manual describes what vienna-rna is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/vienna-rna/vienna-rna.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/vienna-rna/vienna-rna.ps.gz
+
+Format: text
+Files: /usr/share/doc/vienna-rna/vienna-rna.text.gz
+
+Format: HTML
+Index: /usr/share/doc/vienna-rna/html/index.html
+Files: /usr/share/doc/vienna-rna/html/*.html
+
+
Added: trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.install (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,34 @@
+RNAforester/src/RNAforester /usr/bin
+Kinfold/Kinfold /usr/bin
+Progs/RNAeval /usr/bin
+Progs/RNAfold /usr/bin
+Progs/RNAheat /usr/bin
+Progs/RNApaln /usr/bin
+Progs/RNAplot /usr/bin
+Progs/RNAdistance /usr/bin
+Progs/RNAup /usr/bin
+Progs/RNAplfold /usr/bin
+Progs/RNAsubopt /usr/bin
+Progs/RNAalifold /usr/bin
+Progs/RNAaliduplex /usr/bin
+Progs/RNAinverse /usr/bin
+Progs/RNALfold /usr/bin
+Progs/RNApdist /usr/bin
+Progs/RNAcofold /usr/bin
+Progs/RNAduplex /usr/bin
+Utils/Fold /usr/bin
+Utils/b2ct /usr/bin
+Utils/popt /usr/bin
+Utils/ct2b.pl /usr/bin
+Utils/b2mt.pl /usr/bin
+Utils/coloraln.pl /usr/bin
+Utils/rotate_ss.pl /usr/bin
+Utils/colorrna.pl /usr/bin
+Utils/dpzoom.pl /usr/bin
+Utils/cmount.pl /usr/bin
+Utils/mountain.pl /usr/bin
+Utils/refold.pl /usr/bin
+Utils/relplot.pl /usr/bin
+RNAforester/src/RNAforester /usr/bin
+./Readseq/readseq /usr/bin
+./Kinfold/Kinfold /usr/bin
Added: trunk/packages/vienna-rna/trunk/debian/watch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/watch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/watch 2007-11-14 00:56:08 UTC (rev 804)
@@ -0,0 +1,3 @@
+version=3
+http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-(.*)\.tar\.gz
+
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