[med-svn] r459 - trunk/packages/t-coffee/trunk/debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Sun Sep 30 14:46:36 UTC 2007
Author: smoe-guest
Date: 2007-09-30 14:46:36 +0000 (Sun, 30 Sep 2007)
New Revision: 459
Added:
trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base
trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs
trunk/packages/t-coffee/trunk/debian/t-coffee.dirs
Removed:
trunk/packages/t-coffee/trunk/debian/dirs
trunk/packages/t-coffee/trunk/debian/docs
trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base
trunk/packages/t-coffee/trunk/debian/watch
Modified:
trunk/packages/t-coffee/trunk/debian/README.Debian
trunk/packages/t-coffee/trunk/debian/changelog
trunk/packages/t-coffee/trunk/debian/control
trunk/packages/t-coffee/trunk/debian/copyright
trunk/packages/t-coffee/trunk/debian/rules
Log:
[t-coffee]
* update to 5.05
Modified: trunk/packages/t-coffee/trunk/debian/README.Debian
===================================================================
--- trunk/packages/t-coffee/trunk/debian/README.Debian 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/README.Debian 2007-09-30 14:46:36 UTC (rev 459)
@@ -8,9 +8,15 @@
The web interface in the folder html I decided to leave as it is and move
aside the regular documentation. I have not updated the man page from the
-previous version yet. Some helping hands would be welcome in this matter.
+previous version yet. Some helping hands would be welcome in this matter
+and also for the proper description of the accompaning documention in the
+doc-base file. Another issue that comes to mind is the watch file that
+is no longer working for upstream's
+ http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-The example directory was omitted. Should this become a separate package?
+The example directory became a separate package and so are the docs. This
+was motivated by the idea to use Debian packages on compute clusters and
+hence, well, one wants them space-minimal or close to it, at least.
Whenever appropriate please cite this software as
@@ -20,13 +26,13 @@
C. Notredame. Journal of Molecular Biology, Vol 340,
pp385-395, 2004
-or
+and/or
T-Coffee: A novel method for multiple sequence alignments.
C.Notredame, D. Higgins, J. Heringa, Journal of Molecular
Biology,Vol 302, pp205-217, 2000
-or
+and/or
COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
C. Notredame, L. Holme and D.G. Higgins, Bioinformatics, Vol 14
Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/changelog 2007-09-30 14:46:36 UTC (rev 459)
@@ -1,7 +1,10 @@
t-coffee (5.05) unstable; urgency=low
* New upstream version.
+ * Assigned maintainership to Debian-Med.
+ * Moved boxshade from Recommended to Suggested.
* Added use of quilt.
+ * Homepage received its separate line.
-- Steffen Moeller <moeller at debian.org> Mon, 24 Sep 2007 15:05:07 +0200
Modified: trunk/packages/t-coffee/trunk/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/control 2007-09-30 14:46:36 UTC (rev 459)
@@ -1,16 +1,19 @@
Source: t-coffee
Section: science
Priority: optional
-Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
-Build-Depends: debhelper (>= 4.0.0)
-Standards-Version: 3.6.1
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 4.0.0), quilt
+Standards-Version: 3.7.2.1
+XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/
+XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/t-coffee
+Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
Package: t-coffee
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: clustalw, muscle, seaview
-Recommends: boxshade|texshade
-Description: [Biology] Multiple Sequence Alignment
+Suggests: clustalw, muscle, seaview, boxshade, t-coffee-doc
+Description: Multiple Sequence Alignment
T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence
alignment. Version 2.00 and higher can mix sequences and structures.
@@ -20,5 +23,19 @@
estimate the level of consistency of each position within the new
alignment with the rest of the alignments. See the pre-print for more
information
- .
- Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
+
+Package: t-coffee-examples
+Architecture: all
+Recommends: t-coffee
+Description: annotated examples for the use of T-Coffee
+ To help increasing the proficiency in the use of T-Coffee, this
+ package provides examples for input sequences and their proper
+ alignment.
+
+Package: t-coffee-doc
+Architecture: all
+Recommends: t-coffee
+Suggests: t-coffee-examples
+Description: PDF and HTML accompaning documents to T-Coffee
+ The tool for multiple sequence alignment, T-Coffee, is explained
+ both from the users' perspective and for its technical background.
Modified: trunk/packages/t-coffee/trunk/debian/copyright
===================================================================
--- trunk/packages/t-coffee/trunk/debian/copyright 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/copyright 2007-09-30 14:46:36 UTC (rev 459)
@@ -10,7 +10,7 @@
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.
+ the Free Software Foundation in version 2 of the License.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
@@ -19,8 +19,7 @@
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., 59 Temple Place - Suite 330, Boston, MA
- 02111-1307, USA.
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
Deleted: trunk/packages/t-coffee/trunk/debian/dirs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/dirs 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/dirs 2007-09-30 14:46:36 UTC (rev 459)
@@ -1 +0,0 @@
-usr/bin
Deleted: trunk/packages/t-coffee/trunk/debian/docs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/docs 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/docs 2007-09-30 14:46:36 UTC (rev 459)
@@ -1,3 +0,0 @@
-doc/README4T-COFFEE
-doc/*.htm
-html
Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/rules 2007-09-30 14:46:36 UTC (rev 459)
@@ -27,47 +27,56 @@
build-stamp:
dh_testdir
-
- # Add here commands to compile the package.
$(MAKE) -C t_coffee_source -i CC=gcc CFLAGS="$(CFLAGS)" USER_BIN=../bin/ all
- #docbook-to-man debian/t-coffee.sgml > t-coffee.1
-
touch build-stamp
clean: unpatch
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
-
- # Add here commands to clean up after the build process.
$(MAKE) -C t_coffee_source clean
-
dh_clean bin/t_coffee
-install: build
+install: install-arch install-indep
+
+install-arch: build
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
-
dh_install
# Add here commands to install the package into debian/t-coffee.
- cp bin/t_coffee $(CURDIR)/debian/t-coffee/usr/bin/
+ d=$(CURDIR)/debian/t-coffee/usr/bin/ ; \
+ [ -d $$d ] || mkdir -p $$d ; \
+ cp bin/t_coffee $$d
+install-indep:
+
# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
+binary-indep: build install-indep
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ chmod 644 example/*
+ dh_installexamples -pt-coffee-examples example/*
+ dh_link
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
# Build architecture-dependent files here.
-binary-arch: build install
+binary-arch: build install-arch
dh_testdir
dh_testroot
dh_installchangelogs
dh_installdocs
- chmod 644 example/*
- dh_installexamples example
- dh_installman t_coffee.1
+ dh_installman -pt-coffee t_coffee.1
dh_link
dh_strip
dh_compress
Added: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base 2007-09-30 14:46:36 UTC (rev 459)
@@ -0,0 +1,10 @@
+Document: t-coffee
+Title: Debian t-coffee Manual
+Author: Cedric Notredame
+Abstract: A description of T-Coffee, the program
+ for multiple sequence alignment, and sequence
+ formats.
+Section: science
+
+Format: pdf
+Files: /usr/share/doc/t-coffee/t-coffee*.pdf
Added: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs 2007-09-30 14:46:36 UTC (rev 459)
@@ -0,0 +1 @@
+doc/*
Copied: trunk/packages/t-coffee/trunk/debian/t-coffee.dirs (from rev 458, trunk/packages/t-coffee/trunk/debian/dirs)
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee.dirs (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee.dirs 2007-09-30 14:46:36 UTC (rev 459)
@@ -0,0 +1 @@
+usr/bin
Deleted: trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base 2007-09-30 14:46:36 UTC (rev 459)
@@ -1,22 +0,0 @@
-Document: t-coffee
-Title: Debian t-coffee Manual
-Author: Cedric Notredame
-Abstract: A description of T-Coffee, the program
- for multiple sequence alignment, and sequence
- formats.
-Section: science
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/t-coffee/t-coffee.sgml.gz
-
-Format: pdf
-Files: /usr/share/doc/t-coffee/t-coffee*.pdf
-
-Format: text
-Files: /usr/share/doc/t-coffee/*.txt.gz
-
-Format: HTML
-Index: /usr/share/doc/t-coffee/html/index.html
-Files: /usr/share/doc/t-coffee/html/*.html
-
-
Deleted: trunk/packages/t-coffee/trunk/debian/watch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/watch 2007-09-30 09:30:40 UTC (rev 458)
+++ trunk/packages/t-coffee/trunk/debian/watch 2007-09-30 14:46:36 UTC (rev 459)
@@ -1,10 +0,0 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# See uscan(1) for format
-
-# Compulsory line, this is a version 2 file
-version=2
-
-# Uncomment to examine a Webserver directory
-http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution_Version_(.*)\.tar\.gz
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