[med-svn] r1570 - in trunk/packages: . smile smile/trunk smile/trunk/debian smile/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Mar 13 09:04:10 UTC 2008
Author: tille
Date: 2008-03-13 09:04:10 +0000 (Thu, 13 Mar 2008)
New Revision: 1570
Added:
trunk/packages/smile/
trunk/packages/smile/trunk/
trunk/packages/smile/trunk/README
trunk/packages/smile/trunk/debian/
trunk/packages/smile/trunk/debian/README.Debian
trunk/packages/smile/trunk/debian/changelog
trunk/packages/smile/trunk/debian/compat
trunk/packages/smile/trunk/debian/control
trunk/packages/smile/trunk/debian/copyright
trunk/packages/smile/trunk/debian/dirs
trunk/packages/smile/trunk/debian/docs
trunk/packages/smile/trunk/debian/manpages
trunk/packages/smile/trunk/debian/patches/
trunk/packages/smile/trunk/debian/patches/xyz.diff
trunk/packages/smile/trunk/debian/rules
trunk/packages/smile/trunk/debian/watch
Log:
Moved Steffen M?\195?\182llers work which was stalled to svn to keep track of previous work.
Added: trunk/packages/smile/trunk/README
===================================================================
--- trunk/packages/smile/trunk/README (rev 0)
+++ trunk/packages/smile/trunk/README 2008-03-13 09:04:10 UTC (rev 1570)
@@ -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/smile/trunk/debian/README.Debian
===================================================================
--- trunk/packages/smile/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/smile/trunk/debian/README.Debian 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,12 @@
+smile for Debian
+----------------
+
+Renamed SMILE to smile in file names.
+
+The upstream author Laurent Marsan is very supportive of this package
+and being a Debian user himself he even provided a very nice man page
+for the distribution of his package.
+
+Thank you, Laurent!
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Tue, 18 Dec 2003 16:20:05 +0100
Added: trunk/packages/smile/trunk/debian/changelog
===================================================================
--- trunk/packages/smile/trunk/debian/changelog (rev 0)
+++ trunk/packages/smile/trunk/debian/changelog 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,15 @@
+smile (1.47-1) unstable; urgency=low
+
+ * New upstream release.
+ * GPL license stated in upstream release.
+ * Sponsored by Aaron M. Ucko <ucko at debian.org>
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Tue, 05 Apr 2004 13:17:00 +0200
+
+smile (1.46-1) unstable; urgency=low
+
+ * Initial Release (Closes: #221492).
+ * Upstream author contributed man page.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Tue, 18 Nov 2003 16:20:05 +0100
+
Added: trunk/packages/smile/trunk/debian/compat
===================================================================
--- trunk/packages/smile/trunk/debian/compat (rev 0)
+++ trunk/packages/smile/trunk/debian/compat 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1 @@
+4
Added: trunk/packages/smile/trunk/debian/control
===================================================================
--- trunk/packages/smile/trunk/debian/control (rev 0)
+++ trunk/packages/smile/trunk/debian/control 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,28 @@
+Source: smile
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0)
+Standards-Version: 3.6.1.1
+
+Package: smile
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Description: [Biology] Find statistically significant patterns in sequences
+ Smile determines sequence motifs on the basis of a set of DNA, RNA or
+ protein sequences. The work was originally described in the Journal of
+ Computational Biology (2000) 7:345-362 and has since been developed further.
+ .
+ * No hard limit on the number of combinations of motifs to describe
+ subsets of sequences.
+ .
+ * The sequence alphabet may be specified.
+ .
+ * The use of wildcards is supported.
+ .
+ * Better determination of significance of motifs by simulation.
+ .
+ * Introduction of a set of sequences with negative controls
+ that should not match automatically determined motifs.
+ .
+ Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Added: trunk/packages/smile/trunk/debian/copyright
===================================================================
--- trunk/packages/smile/trunk/debian/copyright (rev 0)
+++ trunk/packages/smile/trunk/debian/copyright 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,42 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Tue, 18 Nov 2003 16:20:05 +0100.
+
+It was downloaded from http://www-igm.univ-mlv.fr/~marsan/smile_english.html
+
+Upstream Author: Laurent Marsan <marsan at univ-mlv.fr>
+
+Copyright:
+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public (GPL, Version 2, June 1991)
+ and GNU Less General Public Licenses (LGPL, Version 2.1, February 1999)
+ as published by the Free Software Foundation.
+
+ 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
+ GPL and LGPL for more details.
+
+ You should have received a copy of the GPL and the LGPL
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+ 02111-1307, USA.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'
+and the full text of the Lesser General Public License in
+'/usr/share/common-licenses/LGPL'.
+
+Upstream copyrigh notice from the file COPYING, the Free Software
+Foundation's license files COPYING.gpl and COPYING.lgpl are
+omitted from the packaging:
+
+All the source files of this package are distributed according to the GPL
+License (see COPYING.gpl), except
+ libfasta.h
+ libsysk.h
+ Gtypes.h
+ libfasta.c
+which are distributed according to the LGPL License (see COPYING.lgpl).
+
+
Added: trunk/packages/smile/trunk/debian/dirs
===================================================================
--- trunk/packages/smile/trunk/debian/dirs (rev 0)
+++ trunk/packages/smile/trunk/debian/dirs 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,4 @@
+usr/bin
+usr/lib
+usr/lib/smile
+usr/lib/smile/bin
Added: trunk/packages/smile/trunk/debian/docs
===================================================================
--- trunk/packages/smile/trunk/debian/docs (rev 0)
+++ trunk/packages/smile/trunk/debian/docs 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,17 @@
+Lanceur/READ_ME
+Lanceur/NEW
+Lanceur/1box_deg
+Lanceur/DocFrancais
+Lanceur/NEW
+Lanceur/READ_ME
+Lanceur/alphabet
+Lanceur/alphabet_deg
+Lanceur/example
+Lanceur/example.shuffle
+Lanceur/example2.shuffle
+Lanceur/fasta
+Lanceur/fastawrong
+Lanceur/param_1box
+Lanceur/param_against
+Lanceur/param_delta
+Lanceur/param_example
Added: trunk/packages/smile/trunk/debian/manpages
===================================================================
--- trunk/packages/smile/trunk/debian/manpages (rev 0)
+++ trunk/packages/smile/trunk/debian/manpages 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1 @@
+smile.1
Added: trunk/packages/smile/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/smile/trunk/debian/patches/xyz.diff (rev 0)
+++ trunk/packages/smile/trunk/debian/patches/xyz.diff 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,218 @@
+--- smile-1.47.orig/P_BLOCS/src/allocateurs.c
++++ smile-1.47/P_BLOCS/src/allocateurs.c
+@@ -17,6 +17,7 @@
+ /* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */
+ /******************************************************************************/
+
++#include<unistd.h>
+ #include<allocateurs.h>
+
+ Allocateur Noeud_Alloc;
+--- smile-1.47.orig/P_BLOCS/Makefile
++++ smile-1.47/P_BLOCS/Makefile
+@@ -124,4 +124,12 @@
+ depend:
+ makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
+
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
++
++install: all
++ -mkdir -p $(DESTLIBDIR)/bin
++ cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin
++
++
+ # DO NOT DELETE
+--- smile-1.47.orig/Makefile
++++ smile-1.47/Makefile
+@@ -8,19 +8,26 @@
+
+ all: clean
+ @echo "**** Making P_BLOCS..."
+- (cd $(P_DIR) && $(MAKE) all)
++ $(MAKE) -C $(P_DIR) all
+ @echo "==> P_BLOCS OK."
+ @echo "**** Making P_BLOCS+DELTA..."
+- (cd $(PD_DIR) && $(MAKE) all)
++ $(MAKE) -C $(PD_DIR) all
+ @echo "==> P_BLOCS+DELTA OK."
+ @echo "**** Making SigStat..."
+- (cd $(S_DIR) && $(MAKE) all)
++ $(MAKE) -C $(S_DIR) all
+ @echo "==> SigStat OK."
+
+ clean:
+ @echo Cleaning...
+- (cd $(P_DIR) && $(MAKE) clean)
+- (cd $(PD_DIR) && $(MAKE) clean)
+- (cd $(S_DIR) && $(MAKE) clean)
++ $(MAKE) -C $(P_DIR) clean
++ $(MAKE) -C $(PD_DIR) clean
++ $(MAKE) -C $(S_DIR) clean
+ @echo Clean OK.
+
++DESTDIR=""
++
++install:
++ $(MAKE) -C $(P_DIR) install
++ $(MAKE) -C $(PD_DIR) install
++ $(MAKE) -C $(S_DIR) install
++ cp Lanceur/smile $(DESTDIR)/usr/bin
+--- smile-1.47.orig/P_BLOCS+DELTA/Makefile
++++ smile-1.47/P_BLOCS+DELTA/Makefile
+@@ -124,4 +124,12 @@
+ depend:
+ makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
+
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
++
++install: all
++ -mkdir -p $(DESTLIBDIR)/bin
++ cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin
++
++
+ # DO NOT DELETE
+--- smile-1.47.orig/Lanceur/smile
++++ smile-1.47/Lanceur/smile
+@@ -34,10 +34,22 @@
+ # et symb_compo[i][j] le nb max de ce symbole j apparaissant ds une boite i
+
+ # Chemin des programmes executable ##############################################
+-$prog1 = "../P_BLOCS/bin/x-smile";
+-$prog2 = "../P_BLOCS+DELTA/bin/x-smile_delta";
+-$progstat = "../SigStat/bin/e-smile_shuffling";
+-$progfaux = "../SigStat/bin/e-smile_against";
++
++my $prefix="..";
++if ( -x "/usr/lib/smile/bin") {
++ $prefix="/usr/lib/smile/bin";
++ $prog1 = "$prefix/x-smile";
++ $prog2 = "$prefix/x-smile_delta";
++ $progstat = "$prefix/e-smile_shuffling";
++ $progfaux = "$prefix/e-smile_against";
++}
++else {
++ $prog1 = "$prefix/P_BLOCS/bin/x-smile";
++ $prog2 = "$prefix/P_BLOCS+DELTA/bin/x-smile_delta";
++ $progstat = "$prefix/SigStat/bin/e-smile_shuffling";
++ $progfaux = "$prefix/SigStat/bin/e-smile_against";
++}
++print STDERR "Using binaries in $prefix\n\n";
+
+ # Fichier de noms de fichiers generes ##########################################
+ $namefile = ".namefile";
+--- smile-1.47.orig/SigStat/Makefile
++++ smile-1.47/SigStat/Makefile
+@@ -50,7 +50,7 @@
+
+ grep+::
+ @echo Making grep+...
+- (cd $(GREP_DIR) && $(MAKE) obj)
++ $(MAKE) -C $(GREP_DIR) obj
+ @echo Fin du Make de grep+.
+
+ $(SIG_BIN_DIR)$(PROG_NAME): $(SIG_OBJ)
+@@ -86,7 +86,7 @@
+
+
+ clean: clean_emacs clean_obj
+- (cd $(GREP_DIR) && $(MAKE) clean)
++ $(MAKE) -C $(GREP_DIR) clean
+ @echo CLEAN OK!!!
+
+ clean_emacs:
+@@ -102,3 +102,10 @@
+ tgz: clean
+ tar -zcvf $(ARCHIVE_NAME) ./*
+
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
++
++install: all
++ -mkdir -p $(DESTLIBDIR)/bin
++ cp $(SIG_BIN_DIR)$(PROG_NAME) $(SIG_BIN_DIR)$(PROG_NAME2) $(DESTLIBDIR)/bin
++ $(MAKE) -C $(GREP_DIR) install
+--- smile-1.47.orig/SigStat/grep+/Makefile
++++ smile-1.47/SigStat/grep+/Makefile
+@@ -36,7 +36,7 @@
+
+ SPELL_OBJ=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o
+
+-SPELL_OBJ_DEB=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)main.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o
++SPELL_OBJ_DEB=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)main.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o $(SPELL_OBJ_DIR)/sub_suffix_tree.o
+
+ OBJ_FILE=$(TREE_OBJ) $(SPELL_OBJ)
+
+@@ -132,4 +132,12 @@
+
+ depend:
+ makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
++
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
++
++install: obj
++ #-mkdir -p $(DESTLIBDIR)/bin
++ #cp $(PROG_NAME) $(DESTLIBDIR)/bin
++
+ # DO NOT DELETE
+--- smile-1.47.orig/SigStat/grep+/Spell/src/grep+.c
++++ smile-1.47/SigStat/grep+/Spell/src/grep+.c
+@@ -892,14 +892,14 @@
+
+
+
+-
++#ifdef GREPWITHMAIN
+
+ /******************************************************************************/
+ /******************************************************************************/
+ /********************************** MAIN **************************************/
+ /******************************************************************************/
+ /******************************************************************************/
+-/*
++
+ int main(int argc, char **argv)
+ {
+ Criteres criteres, cr;
+@@ -948,4 +948,4 @@
+
+ return(0);
+ }
+-*/
++#endif
+--- smile-1.47.orig/COPYING
++++ smile-1.47/COPYING
+@@ -1,5 +1,5 @@
+ All the source files of this package are distributed according to the GPL
+-License (see COPYING.gpl), excepted
++License (see COPYING.gpl), except
+ libfasta.h
+ libsysk.h
+ Gtypes.h
+--- smile-1.47.orig/t.paam
++++ smile-1.47/t.paam
+@@ -0,0 +1,22 @@
++
++*********************
++ O o
++ ^ SMILE! v1.47
++ \_/
++*********************
++
++EXTRACTION (Step 1) =======================================================
++FASTA file t.fas
++Output file t.fas_out
++
++GLOBAL PARAMETERS =============
++Alphabet file t.fas_alphabet
++Quorum 90
++Total min length 2
++Total max length 10
++Total substitutions 2
++Boxes 1
++
++Composition in ? 0
++
++
Added: trunk/packages/smile/trunk/debian/rules
===================================================================
--- trunk/packages/smile/trunk/debian/rules (rev 0)
+++ trunk/packages/smile/trunk/debian/rules 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,84 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ zcat smile.1.gz > smile.1
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+ -rm -r $(CURDIR)/debian/smile
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) clean
+ dh_clean smile.1
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/smile.
+ $(MAKE) install DESTDIR=$(CURDIR)/debian/smile
+
+# 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
+ dh_installdocs
+ dh_installexamples
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Added: trunk/packages/smile/trunk/debian/watch
===================================================================
--- trunk/packages/smile/trunk/debian/watch (rev 0)
+++ trunk/packages/smile/trunk/debian/watch 2008-03-13 09:04:10 UTC (rev 1570)
@@ -0,0 +1,5 @@
+# format version number, currently 2; this line is compulsory!
+version=2
+
+# This is one format for an HTTP site, which is the same as the FTP format
+http://www-igm.univ-mlv.fr/~marsan/SMILEv([-0-9\.]*).tgz
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