[med-svn] r2257 - in trunk/packages: . libtfbs-perl libtfbs-perl/trunk libtfbs-perl/trunk/debian libtfbs-perl/trunk/debian/patches
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Fri Jul 18 16:30:27 UTC 2008
Author: smoe-guest
Date: 2008-07-18 16:30:27 +0000 (Fri, 18 Jul 2008)
New Revision: 2257
Added:
trunk/packages/libtfbs-perl/
trunk/packages/libtfbs-perl/trunk/
trunk/packages/libtfbs-perl/trunk/debian/
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/patches/
trunk/packages/libtfbs-perl/trunk/debian/patches/nomysqlserver.patch
trunk/packages/libtfbs-perl/trunk/debian/patches/series
trunk/packages/libtfbs-perl/trunk/debian/rules
trunk/packages/libtfbs-perl/trunk/debian/watch
Log:
Some initial packaging - awaiting reply from upstream still.
Added: trunk/packages/libtfbs-perl/trunk/debian/changelog
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/changelog (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/changelog 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1,5 @@
+libtfbs-perl (0.5.0-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 18 Jul 2008 15:21:37 +0200
Added: trunk/packages/libtfbs-perl/trunk/debian/compat
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/compat (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/compat 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1 @@
+5
Added: trunk/packages/libtfbs-perl/trunk/debian/control
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/control (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/control 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1,19 @@
+Source: libtfbs-perl
+Section: perl
+Priority: optional
+Build-Depends: debhelper (>= 5), perl (>= 5.6.10-12), pdl, quilt
+Maintainer: Steffen Moeller <moeller at debian.org>
+Standards-Version: 3.8.0
+Homepage: http://tfbs.genereg.net
+
+Package: libtfbs-perl
+Architecture: any
+Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, pdl, bioperl
+Description: Perl extension for scanning a DNA sequence object with a position weight matrix
+ Set of routines to interact with the Transfac and Jaspar databases that
+ describe a special family of proteins, the transcription factors. These
+ bind to genomic DNA to initiate (or prevent) the readout of a gene.
+ Once multiple binding sites are known 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.
Added: trunk/packages/libtfbs-perl/trunk/debian/copyright
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/copyright (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/copyright 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1,14 @@
+This is the debian package for the TFBS module.
+It was created by Steffen Moeller <moeller at debian.org> using dh-make-perl.
+
+It was downloaded from http://tfbs.genereg.net.
+
+This Perl module is distributed under the same license as Perl itself.
+Debian summarises the current license on /usr/share/doc/perl/copyright.
+
+The upstream author is:
+
+ Borid Lenhard <Boris.Lenhard at bccs.uib.no>
+
+The Debian packaging is (C) 2008, Steffen Moeller <moeller at debian.org> and
+is licensed under the same terms as the software itself (see above).
Added: trunk/packages/libtfbs-perl/trunk/debian/patches/nomysqlserver.patch
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/patches/nomysqlserver.patch (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/patches/nomysqlserver.patch 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1,16 @@
+Index: tfbs-0.5.0/Makefile.PL
+===================================================================
+--- tfbs-0.5.0.orig/Makefile.PL 2008-07-18 18:13:33.000000000 +0200
++++ tfbs-0.5.0/Makefile.PL 2008-07-18 18:14:02.000000000 +0200
+@@ -21,11 +21,6 @@
+
+ sub get_sql_data {
+ my $ans = "abc";
+- do {
+- print "Do you have write access to a MySQL database server? [n] ";
+- $ans=<STDIN>; chomp $ans;
+- } until $ans =~ /^y|n/i or $ans eq "";
+-
+ if (uc(substr($ans,0,1)) eq 'Y') {
+ print "\nOK, tell me more about it.\n\n";
+ print "\tHost name : [localhost] ";
Added: trunk/packages/libtfbs-perl/trunk/debian/patches/series
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/patches/series (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/patches/series 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1 @@
+nomysqlserver.patch
Added: trunk/packages/libtfbs-perl/trunk/debian/rules
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/rules (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/rules 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1,69 @@
+#!/usr/bin/make -f
+
+export PERL_MM_USE_DEFAULT=1
+
+include /usr/share/quilt/quilt.make
+
+PERL ?= /usr/bin/perl
+PACKAGE = $(shell dh_listpackages)
+TMP = $(CURDIR)/debian/$(PACKAGE)
+
+CFLAGS = -Wall -g
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+Makefile: Makefile.PL
+ $(PERL) Makefile.PL INSTALLDIRS=vendor
+
+build: patch build-stamp
+build-stamp: Makefile
+ dh_testdir
+ # Add commands to compile the package here
+ $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
+ #$(MAKE) test
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ dh_clean build-stamp install-stamp
+ [ -f Makefile ] && $(MAKE) realclean || echo "No Makefile present, assuming prestine setup."
+
+install: install-stamp
+install-stamp: build-stamp
+ dh_testdir
+ dh_testroot
+ 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
+ touch $@
+
+binary-indep: build install
+# We have nothing to do here for an architecture-dependent package
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installexamples examples/*
+ dh_installdocs BUGS README
+ dh_installchangelogs Changes
+ dh_shlibdeps
+ dh_strip
+ dh_perl
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ 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/libtfbs-perl/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libtfbs-perl/trunk/debian/watch
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/watch (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/watch 2008-07-18 16:30:27 UTC (rev 2257)
@@ -0,0 +1,2 @@
+version=3
+http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
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