debian/0000755000000000000000000000000011750573545007202 5ustar debian/watch0000644000000000000000000000012011750571337010221 0ustar version=3 http://www-igm.univ-mlv.fr/~marsan/smile_english.html SMILEv(.*)\.tgz debian/copyright0000644000000000000000000000424711750572064011137 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Alain.Viari@inrialpes.fr Source: http://www-igm.univ-mlv.fr/~marsan/smile_english.html Files: * Copyright: © 2004 L.Marsan (lama@prism.uvsq.fr) License: GPL-2+ This program 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, or (at your option) any later version. . This program 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 GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. Files: P_BLOCS/include/Gtypes.h P_BLOCS/include/libfasta.h P_BLOCS/include/libsysk.h P_BLOCS/src/libfasta.c Copyright: © Atelier de BioInformatique License: LGPL-2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This library 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 GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems, the complete text of the GNU LGPL version 2 can be found in ‘/usr/share/common-licenses/LGPL-2.1’. The mismatch between licence name and license version is verbatim from the source file headers. debian/manpages0000644000000000000000000000001411750571337010710 0ustar mlv-smile.1 debian/dirs0000644000000000000000000000007011750571337010060 0ustar usr/bin usr/lib usr/lib/mlv-smile usr/lib/mlv-smile/bin debian/changelog0000644000000000000000000000347711750573545011067 0ustar mlv-smile (1.47-3) unstable; urgency=low * debian/upstream: Added publication data * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs-Browser - Moved directory in SVN from smile to mlv-smile - Removed citation information from long description - Spacing changes in long description * debian/copyright: Fixed some DEP5 issues using cme fix dpkg-copyright * debhelper 9 (control+compat) to enable hardening * debian/rules: Work around several broken Makefiles that would need fixing by simply redefining CC to enable propagation of hardening flags -- Andreas Tille Thu, 03 May 2012 18:30:20 +0200 mlv-smile (1.47-2) unstable; urgency=low * Spellchecked manual pages (Closes: #650475, thanks to A. Costa). -- Thorsten Alteholz Sat, 03 Dec 2011 19:20:00 +0100 mlv-smile (1.47-1) unstable; urgency=low * initial Release (Closes: #221492). * renamed package to mlv-smile * Lintian clean * already prepared patches from Steffen Moeller applied * debian/source/format added * debian/compat changed to 8 * debian/copyright: new address of FSF, added version to licenses * debian/rules: errors in manpage corrected * debian/rules: simplified * added DEP-3 header to patches [Charles Plessy] * debian/control: Added Vcs fields * debian/control: Removed the [Biology] tag in the package short description * debian/copyright: Converted the copyright file to DEP-5 format [Steffen Moeller] * New upstream release. * GPL license stated in upstream release. -- Thorsten Alteholz Tue, 18 May 2011 18:17:00 +0200 mlv-smile (1.46-1) UNRELEASED; urgency=low * Upstream author contributed man page. -- Steffen Moeller Tue, 18 Nov 2003 16:20:05 +0100 debian/README.Debian0000644000000000000000000000101711750571337011237 0ustar smile for Debian ---------------- As there is a multimedia package with the same name, I renamed this package to mlv-smile. -- Thorsten Alteholz , Wed, 18 May 2011 18:20:05 +0200 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 , Tue, 18 Dec 2003 16:20:05 +0100 debian/source/0000755000000000000000000000000011750567166010504 5ustar debian/source/format0000644000000000000000000000001411750567012011700 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211750572615010375 0ustar 9 debian/patches/0000755000000000000000000000000011750567166010633 5ustar debian/patches/series0000644000000000000000000000005111750567012012032 0ustar Makefile.patch although.patch misc.patch debian/patches/although.patch0000644000000000000000000000123111750567012013452 0ustar Desription: Spelling error altough -> although Author: Thorsten Alteholz Last-Update: 2011-05-20 --- smile-1.47.orig/SigStat/src/io.c 2011-05-16 18:18:45.000000000 +0200 +++ smile-1.47/SigStat/src/io.c 2011-05-16 18:20:30.000000000 +0200 @@ -132,7 +132,7 @@ fprintf(stderr, "Error: output file contains no occurrences number,\n"); fprintf(stderr, - " altough statistics on total number of occurrences have been requested.\n"); + " although statistics on total number of occurrences have been requested.\n"); return (NULL); } else debian/patches/Makefile.patch0000644000000000000000000000706511750567012013367 0ustar Desription: Add install target to Makefiles Author: Steffen Moeller Last-Update: 2011-05-20 --- 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/mlv-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/mlv-smile --- 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/mlv-smile/ + +install: all + -mkdir -p $(DESTLIBDIR)/bin + cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin + + # DO NOT DELETE --- 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/mlv-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/mlv-smile/ + +install: obj + #-mkdir -p $(DESTLIBDIR)/bin + #cp $(PROG_NAME) $(DESTLIBDIR)/bin + # DO NOT DELETE debian/patches/misc.patch0000644000000000000000000000553711750567012012607 0ustar Desription: Different patches for Debian. Author: Steffen Moeller Last-Update: 2011-05-20 --- smile-1.47.orig/P_BLOCS/src/allocateurs.c +++ smile-1.47/P_BLOCS/src/allocateurs.c @@ -17,6 +17,7 @@ /* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ /******************************************************************************/ +#include #include Allocateur Noeud_Alloc; --- smile-1.47.orig/Lanceur/smile +++ smile-1.47/Lanceur/smile @@ -34,10 +34,22 @@ # et symb_compo[i][j] le nb max de ce symbole j apparaissant ds une boite i # Chemin des programmes executable ############################################## -$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/mlv-smile/bin") { + $prefix="/usr/lib/mlv-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/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 + + debian/rules0000755000000000000000000000167311750572671010270 0ustar #!/usr/bin/make -f # debian/rules file for smile # Thorsten Alteholz # GPL %: dh $@ override_dh_auto_build: dh_auto_build -- CC="gcc $(CPPFLAGS) $(CFLAGS) $(LDFLAGS)" override_dh_auto_install: zcat smile.1.gz |sed "s/\.\.\.which/which/g"|\ sed "s/repecting/respecting/g"|\ sed "s/susbtitutions/substitutions/g"|\ sed "s/alindrom/alindrome/g"|\ sed "s/ipossible/possible/g"|\ sed "s/smalls/small/g"|\ sed "s/nfering/nferring/g"|\ sed "s/criterias/criteria/g"|\ sed "s/CRITERIAS/CRITERIA/g"|\ sed "s/allows to/allows one to/g"|\ sed "s/algorithmical/algorithmically/g"|\ sed "s/smile \-g/smile \\\-g/g"|\ sed "s/smile/mlv-smile/g"|\ sed "s/Smile/mlv-smile/g" > mlv-smile.1 dh_installchangelogs READ_ME dh_auto_install debian/control0000644000000000000000000000223411750572627010606 0ustar Source: mlv-smile Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Thorsten Alteholz , Andreas Tille Build-Depends: debhelper (>= 9) Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mlv-smile/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mlv-smile/trunk/ Standards-Version: 3.9.3 Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html Package: mlv-smile Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, perl Description: Find statistically significant patterns in sequences Smile determines sequence motifs on the basis of a set of DNA, RNA or protein sequences. * 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. debian/docs0000644000000000000000000000047011750571337010053 0ustar 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 debian/upstream0000644000000000000000000000273511750571337010771 0ustar Reference: - Author: L. Marsan and M.-F. Sagot Title: Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification Journal: J. of Comput. Biol. Year: 2000 Volume: 7 Number: 3-4 Pages: 345-362 DOI: 10.1089/106652700750050826 PMID: 11108467 URL: http://online.liebertpub.com/doi/abs/10.1089/106652700750050826 eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/106652700750050826 - Author: A. Vanet and L. Marsan and M.-F. Sagot Title: Promoter sequences and algorithmical methods for identifying them Journal: Research in Microbiology Year: 1999 Volume: 150 Number: 9-10 Pages: 779-799 DOI: 10.1016/S0923-2508(99)00115-1 PMID: 10673015 URL: http://www.sciencedirect.com/science/article/pii/S0923250899001151 - Author: A. Vanet and L. Marsan and A. Labigne and M.-F. Sagot Title: Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals. Journal: J. Mol. Biol. Year: 2000 Volume: 297 Number: 2 Pages: 335-353 DOI: 10.1006/jmbi.2000.3576 PMID: 10715205 URL: http://www.sciencedirect.com/science/article/pii/S0022283600935769 - Author: D. Arquès and J.-P. Fallot and L. Marsan and C. Michel Title: An evolutionary analytical model of a complementary circular code Journal: Biosystems Year: 1999 Volume: 49 Number: 2 Pages: 83-103 PMID: 10203190