Author: plessy
Date: 2008-08-03 07:28:06 +0000 (Sun, 03 Aug 2008)
New Revision: 2377
Removed:
trunk/packages/libtfbs-perl/trunk/debian/patches/
Modified:
trunk/packages/libtfbs-perl/trunk/debian/changelog
trunk/packages/libtfbs-perl/trunk/debian/compat
trunk/packages/libtfbs-perl/trunk/debian/control
trunk/packages/libtfbs-perl/trunk/debian/copyright
trunk/packages/libtfbs-perl/trunk/debian/rules
Log:
Fixed dependency relationships, rewrote copyright file, refreshed rules,
replaced patches by equivalent mechanism.
* debian/control:
- Added bioperl to the build dependencies (Closes: #493341).
- Dropped quilt build dependency (see below).
- Added myself to the Uploaders field.
- Added `libgd-gd2-perl | libgd-gd2-noxpm-perl' as recommended package.
* debian/compat, debian/control:
- Using debhelper 7.
* debian/rules:
- Refreshed with `dh-make-perl --refresh'.
* debian/patches, debian/rules:
- Disabling the MySQL tests with `echo "n" |' instead of patches.
* debian/copyright:
- Converted to machine-readable format.
- Added myself to the Hall of Fame.
My hard drive is full, I will cowbuild the package at work and upload from
there.
Modified: trunk/packages/libtfbs-perl/trunk/debian/changelog
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/changelog 2008-08-01 09:12:16 UTC
(rev 2376)
+++ trunk/packages/libtfbs-perl/trunk/debian/changelog 2008-08-03 07:28:06 UTC
(rev 2377)
@@ -1,3 +1,22 @@
+libtfbs-perl (0.5.svn.20080722-2) unstable; urgency=low
+
+ * debian/control:
+ - Added bioperl to the build dependencies (Closes: #493341).
+ - Dropped quilt build dependency (see below).
+ - Added myself to the Uploaders field.
+ - Added `libgd-gd2-perl | libgd-gd2-noxpm-perl' as recommended package.
+ * debian/compat, debian/control:
+ - Using debhelper 7.
+ * debian/rules:
+ - Refreshed with `dh-make-perl --refresh'.
+ * debian/patches, debian/rules:
+ - Disabling the MySQL tests with `echo "n" |' instead of patches.
+ * debian/copyright:
+ - Converted to machine-readable format.
+ - Added myself to the Hall of Fame.
+
+ -- Charles Plessy <[EMAIL PROTECTED]> Sun, 03 Aug 2008 15:38:41 +0900
+
libtfbs-perl (0.5.svn.20080721-1) unstable; urgency=low
* Initial Release.
Modified: trunk/packages/libtfbs-perl/trunk/debian/compat
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/compat 2008-08-01 09:12:16 UTC
(rev 2376)
+++ trunk/packages/libtfbs-perl/trunk/debian/compat 2008-08-03 07:28:06 UTC
(rev 2377)
@@ -1 +1 @@
-5
+7
Modified: trunk/packages/libtfbs-perl/trunk/debian/control
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/control 2008-08-01 09:12:16 UTC
(rev 2376)
+++ trunk/packages/libtfbs-perl/trunk/debian/control 2008-08-03 07:28:06 UTC
(rev 2377)
@@ -1,16 +1,17 @@
Source: libtfbs-perl
Section: perl
Priority: optional
-Build-Depends: debhelper (>= 5), perl (>= 5.6.10-12), pdl, quilt
+Build-Depends: debhelper (>= 7), perl (>= 5.6.10-12), pdl, bioperl
Maintainer: Debian-Med Packaging Team <[EMAIL PROTECTED]>
DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <[EMAIL PROTECTED]>
+Uploaders: Steffen Moeller <[EMAIL PROTECTED]>, Charles Plessy <[EMAIL
PROTECTED]>
Standards-Version: 3.8.0
Homepage: http://tfbs.genereg.net
Package: libtfbs-perl
Architecture: any
Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, pdl, bioperl
+Recommends: libgd-gd2-perl | libgd-gd2-noxpm-perl
Description: scanning DNA sequence with a position weight matrix
The TFBS perl modules comprise a set of routines to interact with the
Transfac and Jaspar databases that describe a special family of proteins,
@@ -19,3 +20,7 @@
for a transcription factor, these are gathered in a single file and are
aligned in order to find position-specific characteristica that might
be used to predict such binding events in novel DNA sequences.
+ .
+ If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002)
+ TFBS: Computational framework for transcription factor binding site analysis.
+ Bioinformatics 18:1135-1136".
Modified: trunk/packages/libtfbs-perl/trunk/debian/copyright
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/copyright 2008-08-01 09:12:16 UTC
(rev 2376)
+++ trunk/packages/libtfbs-perl/trunk/debian/copyright 2008-08-03 07:28:06 UTC
(rev 2377)
@@ -1,21 +1,32 @@
-This is the debian package for the TFBS module.
-It was created by Steffen Moeller <[EMAIL PROTECTED]> using dh-make-perl.
+Format-Specification:
http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=226
+Upstream-Name: TFBS
+Upstream-Maintainer: Boris Lenhard <[EMAIL PROTECTED]>
+Upstream-Source: http://www.ii.uib.no/svn/lenhard/TFBS/
+Packaged-by: Steffen Moeller <[EMAIL PROTECTED]>
+Packaged-date: Fri, 18 Jul 2008 15:21:37 +0200
-It was downloaded from http://tfbs.genereg.net.
+Files: *
+Copyright: © 2005-2007 Boris Lenhard <[EMAIL PROTECTED]>,
+ Stephen Montgomery <[EMAIL PROTECTED]>,
+ Leonardo Marino-Ramirez,
+ Wynand Alkema,
+License: Artistic | GPL1+
+ This Perl module is distributed under the same license as Perl itself.
+X-Comment: Perl license:
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of either:
+ .
+ a) the GNU General Public License as published by the Free Software
+ Foundation; either version 1, or (at your option) any later
+ version, or
+ .
+ b) the "Artistic License" which comes with Perl.
+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' and the
+ Artistic Licence in `/usr/share/common-licenses/Artistic'.
-This Perl module is distributed under the same license as Perl itself.
-Debian summarises the current license on /usr/share/doc/perl/copyright.
-
-The lead upstream author is:
-
- Borid Lenhard <[EMAIL PROTECTED]>
-
-with contributions by
-
- Stephen Montgomery <[EMAIL PROTECTED]>
- Leonardo Marino-Ramirez
- Wynand Alkema
-
-
-The Debian packaging is (C) 2008, Steffen Moeller <[EMAIL PROTECTED]> and
-is licensed under the same terms as the software itself (see above).
+Files: debian/*
+Copyright: © 2008 Steffen Moeller <[EMAIL PROTECTED]>
+ © 2008 Charles Plessy <[EMAIL PROTECTED]>
+License: same as TFBS itself
+ (see above)
Modified: trunk/packages/libtfbs-perl/trunk/debian/rules
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/rules 2008-08-01 09:12:16 UTC
(rev 2376)
+++ trunk/packages/libtfbs-perl/trunk/debian/rules 2008-08-03 07:28:06 UTC
(rev 2377)
@@ -1,13 +1,22 @@
#!/usr/bin/make -f
+# This debian/rules file is provided as a template for normal perl
+# packages. It was created by Marc Brockschmidt <[EMAIL PROTECTED]> for
+# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may
+# be used freely wherever it is useful.
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# If set to a true value then MakeMaker's prompt function will
+# always return the default without waiting for user input.
export PERL_MM_USE_DEFAULT=1
-include /usr/share/quilt/quilt.make
-
PERL ?= /usr/bin/perl
PACKAGE = $(shell dh_listpackages)
TMP = $(CURDIR)/debian/$(PACKAGE)
+# Allow disabling build optimisation by setting noopt in
+# $DEB_BUILD_OPTIONS
CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
@@ -15,22 +24,21 @@
CFLAGS += -O2
endif
-Makefile: Makefile.PL
- $(PERL) Makefile.PL INSTALLDIRS=vendor
-
-build: patch build-stamp
-build-stamp: Makefile
+build: build-stamp
+build-stamp:
dh_testdir
# Add commands to compile the package here
+ echo "n" | $(PERL) Makefile.PL INSTALLDIRS=vendor
$(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
- #$(MAKE) test
+ $(MAKE) test
touch $@
-clean: unpatch
+clean:
dh_testdir
dh_testroot
dh_clean build-stamp install-stamp
- [ -f Makefile ] && $(MAKE) realclean || echo "No Makefile present,
assuming prestine setup."
+ # Add commands to clean up after the build process here
+ [ ! -f Makefile ] || $(MAKE) realclean
install: install-stamp
install-stamp: build-stamp
@@ -39,16 +47,16 @@
dh_clean -k
# Add commands to install the package into $(TMP)
$(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
- if [ -d $(TMP)/usr/share/perl5 ]; then \
- rmdir --ignore-fail-on-non-empty --parents --verbose
$(TMP)/usr/share/perl5; \
- else \
- echo "No install directory to clean"; \
- fi
+ [ ! -d $(TMP)/usr/share/perl5 ] || \
+ rmdir --ignore-fail-on-non-empty --parents --verbose \
+ $(TMP)/usr/share/perl5
touch $@
+# Build architecture-independent files here.
binary-indep: build install
# We have nothing to do here for an architecture-dependent package
+# Build architecture-dependent files here.
binary-arch: build install
dh_testdir
dh_testroot
@@ -71,6 +79,5 @@
svn co http://www.ii.uib.no/svn/lenhard/TFBS/ ../$$n-$$v ; \
cd ..; tar --exclude=.svn -czvf $${n}_$${v}.orig.tar.gz $$n-$$v
-
binary: binary-indep binary-arch
.PHONY: build clean binary-indep binary-arch binary install
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