[med-svn] r1824 - trunk/packages/exonerate/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Mon May 5 04:09:38 UTC 2008
Author: plessy
Date: 2008-05-05 04:09:37 +0000 (Mon, 05 May 2008)
New Revision: 1824
Removed:
trunk/packages/exonerate/trunk/debian/dirs
Modified:
trunk/packages/exonerate/trunk/debian/changelog
trunk/packages/exonerate/trunk/debian/control
trunk/packages/exonerate/trunk/debian/copyright
trunk/packages/exonerate/trunk/debian/docs
trunk/packages/exonerate/trunk/debian/exonerate.manpages
trunk/packages/exonerate/trunk/debian/rules
Log:
Preparing new upstream release, and switching the package to CDBS.
Modified: trunk/packages/exonerate/trunk/debian/changelog
===================================================================
--- trunk/packages/exonerate/trunk/debian/changelog 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/changelog 2008-05-05 04:09:37 UTC (rev 1824)
@@ -1,12 +1,33 @@
-exonerate (1.4.0-2) UNRELEASED; urgency=low
+exonerate (2.0.0-1) UNRELEASED; urgency=low
[ David Paleino ]
* Updated to Standards-Version 3.7.3 (no changes needed)
[ Charles Plessy ]
+ * New upstream release (Closes: #479323)
+ Quoting the upstream changelog:
+ o Modified exonerate to work in Client:Server mode
+ o Fixed --refine to work with SDP alignments
+ o Disabled codegen warnings from bootstrapper during compilation
+ o Added --geneticcode option for using alternative genetic codes
+ o Added --splice5 and --splice3 to allow alternative splice site PSSMs
+ o Fixed several bugs when scanning query sequences (eg. --forcescan query)
+ o Fixed to report query on forward strand whenever possible.
+ o Fixed --ryo sequence dumping with --bestn
+ o Fixed a bug with missing seeds when using --annotation
+ o Changed license to GPLv3
+ o Added protein2dna:bestfit and protein2genome:bestfit models
+ (works with exhaustive alignment only)
* Updated my email address.
+ * debian/control:
+ - Building on glib-2.0 instead of 1.2.
+ - Augmented the long description and changed the short.
+ - Added a build dependency on CDBS.
+ * debian/copyright made machine-readable.
+ * debian/rules switched to cdbs.
+ * debian/dirs: removed.
- -- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 17:01:01 +0900
+ -- Charles Plessy <plessy at debian.org> Sun, 04 May 2008 22:23:18 +0900
exonerate (1.4.0-1) unstable; urgency=low
Modified: trunk/packages/exonerate/trunk/debian/control
===================================================================
--- trunk/packages/exonerate/trunk/debian/control 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/control 2008-05-05 04:09:37 UTC (rev 1824)
@@ -4,7 +4,7 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 5), autotools-dev, libglib1.2-dev
+Build-Depends: debhelper (>= 5), autotools-dev, libglib2.0-dev, cdbs
Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/exonerate/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/exonerate/trunk/
@@ -14,10 +14,18 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Suggests: wise
-Description: tool for comparison of long biological sequences
- Much of the functionality of the Wise dynamic programming
- suite was reimplemented in C for better efficiency.
- Exonerate is an intrinsic component of the building of
- the Ensembl genome databases, providing similarity
- scores between RNA and DNA sequences and thus determining
- splice variants and coding sequences in general.
+Description: generic tool for pairwise sequence comparison
+ Exonerate allows you to align sequences using a many alignment models, using
+ either exhaustive dynamic programming, or a variety of heuristics. Much of
+ the functionality of the Wise dynamic programming suite was reimplemented in C
+ for better efficiency. Exonerate is an intrinsic component of the building of
+ the Ensembl genome databases, providing similarity scores between RNA and DNA
+ sequences and thus determining splice variants and coding sequences in
+ general.
+ .
+ An In-silico PCR Experiment Simulation System (see the ipcress man page) is
+ packaged with exonerate.
+ .
+ This package also comes with a selection of utilities for performing
+ simple manipulations quickly on fasta files beyond 2Gb
+
Modified: trunk/packages/exonerate/trunk/debian/copyright
===================================================================
--- trunk/packages/exonerate/trunk/debian/copyright 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/copyright 2008-05-05 04:09:37 UTC (rev 1824)
@@ -1,38 +1,35 @@
-This package was debianized by Steffen Moeller <moeller at debian.org> on
-Mon, 02 Jul 2007 11:42:38 +0200.
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: This package was debianized by Steffen Moeller <moeller at debian.org>
+Debianized-Date: Mon, 02 Jul 2007 11:42:38 +0200
+Original-Source-Location: http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.0.0.tar.gz
+Upstream-Author: Guy St. C. Slater <guy at ebi.ac.uk>
+ The following have contributed code to this project:
+ (in chronological order)
+ Ewan Birney <birney at ebi.ac.uk>
+ Ian Holmes <ihh at fruitfly.org>
+ Steve Searle <searle at sanger.ac.uk>
+ Tim Cutts <tjrc at sanger.ac.uk>
-It was downloaded from http://www.ebi.ac.uk/~guy/exonerate/
+Files: *
+Copyright: © 2000-2008 Guy St. C. Slater
+License: GPL-3+
+ 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 program 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 <http://www.gnu.org/licenses/>.
+X-Comment: On Debian GNU/Linux systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'
-Upstream Author:
-
- Guy St. C. Slater <guy at ebi.ac.uk>
-
-Copyright:
-
- Copyright (C) 2000-2006 Guy St. C. Slater
-
-License:
-
- This package is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser 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
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser 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 Lesser General
-Public License can be found in `/usr/share/common-licenses/LGPL'.
-The source code of this package links to the web URL indicating
-to version 3 of the license. The author is likely not to have been
-aware of the new version at the time the source code was released.
-The version distributed with the source is an earlier version.
-
-The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
-is licensed under the LGPL, see `/usr/share/common-licenses/LGPL'.
+Files: debian/*
+Copyright: © 2007 Steffen Moeller <moeller at debian.org>
+ © 2008 Charles Plessy <plessy at debian.org>
+License: GPL-3+
+ (see above)
Deleted: trunk/packages/exonerate/trunk/debian/dirs
===================================================================
--- trunk/packages/exonerate/trunk/debian/dirs 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/dirs 2008-05-05 04:09:37 UTC (rev 1824)
@@ -1 +0,0 @@
-usr/bin
Modified: trunk/packages/exonerate/trunk/debian/docs
===================================================================
--- trunk/packages/exonerate/trunk/debian/docs 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/docs 2008-05-05 04:09:37 UTC (rev 1824)
@@ -1,4 +1,4 @@
-NEWS
README
TODO
AUTHORS
+ChangeLog
Modified: trunk/packages/exonerate/trunk/debian/exonerate.manpages
===================================================================
--- trunk/packages/exonerate/trunk/debian/exonerate.manpages 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/exonerate.manpages 2008-05-05 04:09:37 UTC (rev 1824)
@@ -1,3 +1,2 @@
-doc/man/man1/exonerate.1
-doc/man/man1/ipcress.1
+doc/man/man1/*.1
debian/manpages/fastaoverlap.1
Modified: trunk/packages/exonerate/trunk/debian/rules
===================================================================
--- trunk/packages/exonerate/trunk/debian/rules 2008-05-04 07:27:08 UTC (rev 1823)
+++ trunk/packages/exonerate/trunk/debian/rules 2008-05-05 04:09:37 UTC (rev 1824)
@@ -1,116 +1,8 @@
#!/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
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+DEB_CONFIGURE_EXTRA_FLAGS := --enable-glib2
-# 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 ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-
-
-CFLAGS = -Wall -g
-
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-config.status: configure
- dh_testdir
- # Add here commands to configure the package.
-ifneq "$(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="$(CFLAGS)"
- #--disable-glib2
-
- #./configure --host="$(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/exonerate.sgml > exonerate.1
-
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp
-
- # Add here commands to clean up after the build process.
- [ ! -f Makefile ] || $(MAKE) distclean
- rm -f config.sub config.guess
- rm -rf codegen
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
- # Add here commands to install the package into debian/exonerate.
- $(MAKE) DESTDIR=$(CURDIR)/debian/exonerate 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 # Installs three manpages
- dh_link # Makes symlinks to a common manpage
- 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
+# rm -rf codegen
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