[med-svn] r1576 - in trunk/packages: . tfbs tfbs/trunk tfbs/trunk/debian tfbs/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Mar 13 12:51:43 UTC 2008
Author: tille
Date: 2008-03-13 12:51:42 +0000 (Thu, 13 Mar 2008)
New Revision: 1576
Added:
trunk/packages/tfbs/
trunk/packages/tfbs/trunk/
trunk/packages/tfbs/trunk/README
trunk/packages/tfbs/trunk/debian/
trunk/packages/tfbs/trunk/debian/README.Debian
trunk/packages/tfbs/trunk/debian/changelog
trunk/packages/tfbs/trunk/debian/compat
trunk/packages/tfbs/trunk/debian/control
trunk/packages/tfbs/trunk/debian/copyright
trunk/packages/tfbs/trunk/debian/patches/
trunk/packages/tfbs/trunk/debian/patches/xyz.diff
trunk/packages/tfbs/trunk/debian/rules
trunk/packages/tfbs/trunk/debian/watch
Log:
Moved Steffen M?\195?\182llers work which was stalled to svn to keep track of previous work.
Added: trunk/packages/tfbs/trunk/README
===================================================================
--- trunk/packages/tfbs/trunk/README (rev 0)
+++ trunk/packages/tfbs/trunk/README 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,3 @@
+Work on this project was started by Steffen Möller but has stalled.
+Feel free to take it over.
+
Added: trunk/packages/tfbs/trunk/debian/README.Debian
===================================================================
--- trunk/packages/tfbs/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/tfbs/trunk/debian/README.Debian 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,7 @@
+The license information was passed in a personal email from the upstream
+authors, promising to include such with the next upstream release.
+
+Steffen
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Mon, 1 Aug 2005 18:22:23 +0200
+
Added: trunk/packages/tfbs/trunk/debian/changelog
===================================================================
--- trunk/packages/tfbs/trunk/debian/changelog (rev 0)
+++ trunk/packages/tfbs/trunk/debian/changelog 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,6 @@
+tfbs (0.5.0-1) unstable; urgency=low
+
+ * Initial Release (Closes: Bug#320777).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Mon, 1 Aug 2005 18:22:23 +0200
+
Added: trunk/packages/tfbs/trunk/debian/compat
===================================================================
--- trunk/packages/tfbs/trunk/debian/compat (rev 0)
+++ trunk/packages/tfbs/trunk/debian/compat 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1 @@
+4
Added: trunk/packages/tfbs/trunk/debian/control
===================================================================
--- trunk/packages/tfbs/trunk/debian/control (rev 0)
+++ trunk/packages/tfbs/trunk/debian/control 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,41 @@
+Source: tfbs
+Section: perl
+Priority: optional
+Build-Depends: debhelper (>= 4.0.2), perl (>= 5.8.0-7), bioperl (>= 1.0.0)
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Standards-Version: 3.6.2
+
+Package: libtfbs-perl
+Architecture: any
+Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, bioperl (>= 1.0.0)
+Suggests: meme
+Description: [Biology] Perl extension for scanning a DNA sequences for TFBS
+ TFBS Perl OO modules implement classes for the representation of objects
+ encountered in analysis of protein-binding sites in DNA sequences.The
+ objects defined by TFBS classes include:
+ * pattern definition objects, currently position specific score matrices
+ (raw frequency, information content and position weight matrices)with
+ methods for interconversion between matrix types, sequence searching
+ with a matrix profile, sequence 'logo' drawing and matrix manipulation;
+ * a composite object representing a set of position specific score
+ matrices, with methods for the identification of motifs within DNA
+ sequences with the set of profiles from its member matrices;
+ * methods for searching pairwise alignments for patterns conserved
+ in both sequences (phylogenetic footprinting) defined for both matrix
+ profile and composite (matrix set) objects;
+ * an object representing DNA binding site sequence, and an object
+ representing sets of DNA binding sequences, with methods and helper
+ classes to facilitate scanning, filtering and statistical analyses;
+ * an object representing a pair of DNA binding site sequences, and an
+ object representing a set of such pairs, for storage, manipulation and
+ analysis of phylogenetic footprinting searches;
+ * database interfaces to relational, flat file and WWW database of
+ position-specifc score matrices, with methods for searching existing
+ databases, as well as creating new ones containing user-defined matrices.
+ * interfaces to matrix pattern generating programs
+ .
+ The modules within the TFBS set are fully integrated and compatible with
+ Bioperl.
+ .
+ Homepage: http://forkhead.cgb.ki.se/TFBS/
+
Added: trunk/packages/tfbs/trunk/debian/copyright
===================================================================
--- trunk/packages/tfbs/trunk/debian/copyright (rev 0)
+++ trunk/packages/tfbs/trunk/debian/copyright 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,22 @@
+This is the debian package for the TFBS perl module.
+It was created by Steffen Moeller <moeller at pzr.uni-rostock.de> using dh-make-perl.
+
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Mon, 1 Aug 2005.
+
+It was downloaded from http://forkhead.cgb.ki.se/TFBS/
+
+Copyright Holder: Boris Lenhard <Boris.Lenhard at cgb.ki.se>
+
+License:
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the "Artistic License" which comes with Debian.
+
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+ OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+On Debian systems, the complete text of the Artistic License
+can be found in `/usr/share/common-licenses/Artistic'.
+
Added: trunk/packages/tfbs/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/tfbs/trunk/debian/patches/xyz.diff (rev 0)
+++ trunk/packages/tfbs/trunk/debian/patches/xyz.diff 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,34 @@
+--- tfbs-0.5.0.orig/Makefile.PL
++++ tfbs-0.5.0/Makefile.PL
+@@ -16,15 +16,17 @@
+ SUFFIX => '.gz',
+ DIST_DEFAULT => 'all tardist',
+ },
+-
++ ABSTRACT => "classes for analysis of protein-binding sites in DNA sequences",
+ );
+
+ 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 "";
++ #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 "";
++ $ans="n";
+
+ if (uc(substr($ans,0,1)) eq 'Y') {
+ print "\nOK, tell me more about it.\n\n";
+@@ -38,7 +40,7 @@
+
+ print "\tPassword : [none] ";
+ my $password = <STDIN>; chomp $password;
+- $password = '' unless password;
++ $password = '' unless $password;
+
+ open FILE, ">t/MYSQLCONNECT"
+ or die "Can't write to t/ directory, stopped";
Added: trunk/packages/tfbs/trunk/debian/rules
===================================================================
--- trunk/packages/tfbs/trunk/debian/rules (rev 0)
+++ trunk/packages/tfbs/trunk/debian/rules 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,94 @@
+#!/usr/bin/make -f
+# This debian/rules file is provided as a template for normal perl
+# packages. It was created by Marc Brockschmidt <marc at dch-faq.de> for
+# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may
+# be used freely wherever it is useful.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# If set to a true value then MakeMaker's prompt function will
+# always return the default without waiting for user input.
+export PERL_MM_USE_DEFAULT=1
+
+PACKAGE=$(shell dh_listpackages)
+
+ifndef PERL
+PERL = /usr/bin/perl
+endif
+
+TMP =$(CURDIR)/debian/$(PACKAGE)
+
+# Allow disabling build optimation by setting noopt in
+# $DEB_BUILD_OPTIONS
+CFLAGS = -Wall -g
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+build: build-stamp
+build-stamp:
+ dh_testdir
+
+ # Add commands to compile the package here
+ $(PERL) Makefile.PL INSTALLDIRS=vendor
+ $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+
+ # Add commands to clean up after the build process here
+ -$(MAKE) realclean
+
+ dh_clean build-stamp install-stamp Makefile.old Makefile
+
+install: build install-stamp
+install-stamp:
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+
+ # Add commands to install the package into debian/$PACKAGE_NAME here
+ $(MAKE) test
+ $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
+
+ # As this is a architecture dependent package, we are not
+ # supposed to install stuff to /usr/share. MakeMaker creates
+ # the dirs, we delete them from the deb:
+ rmdir --ignore-fail-on-non-empty --parents $(TMP)/usr/share/perl5
+
+ touch install-stamp
+
+# 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_installdocs BUGS README
+ dh_installexamples
+ dh_installchangelogs Changes
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_makeshlibs
+ dh_installdeb
+ dh_perl
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+source diff:
+ @echo >&2 'source and diff are obsolete - use dpkg-source -b'; false
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary
Added: trunk/packages/tfbs/trunk/debian/watch
===================================================================
--- trunk/packages/tfbs/trunk/debian/watch (rev 0)
+++ trunk/packages/tfbs/trunk/debian/watch 2008-03-13 12:51:42 UTC (rev 1576)
@@ -0,0 +1,2 @@
+version=3
+http://forkhead.cgb.ki.se/TFBS/TFBS-([0-9.]+)\.tar\.gz
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