debian/0000755000000000000000000000000012221071652007164 5ustar debian/control0000644000000000000000000000332512215607656010606 0ustar Source: cluster3 Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Thorsten Alteholz Build-Depends: debhelper (>= 9), libmotif-dev, autotools-dev, perl, libx11-dev, libice-dev, libxext-dev, libsm-dev, libxt-dev, docbook-to-man Standards-Version: 3.9.4 Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/cluster3/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cluster3/trunk/ Package: cluster3 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: treeview Suggests: mapleview, smile Description: Reimplementation of the Eisen-clustering software The open source clustering software available here contains clustering routines that can be used to analyze gene expression data. Routines for hierarchical (pairwise simple, complete, average, and centroid linkage) clustering, k-means and k-medians clustering, and 2D self-organizing maps are included. The routines are available in the form of a C clustering library, an extension module to Python, a module to Perl, as well as an enhanced version of Cluster, which was originally developed by Michael Eisen of Berkeley Lab. The C clustering library and the associated extension module for Python was released under the Python license. The Perl module was released under the Artistic License. Cluster 3.0 is covered by the original Cluster/TreeView license. . This package only contains the command line and motif gui versions of Cluster 3.0. debian/copyright0000644000000000000000000000444412125621012011117 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: cluster Upstream-Contact: M. J. L. de Hoon Source: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm Files: * Copyright: M. J. L. de Hoon , S. Imoto, J. Nolan, and S. Miyano, Michael Eisen License: different The Open Source Clustering Software consists of several packages, which have different licenses. . * Cluster 3.0 is a GUI-based program for Windows, Mac OS X, Linux, and Unix. It is based on Michael Eisen's Cluster/TreeView code. Cluster 3.0 is covered by Michael Eisen's original license, available at http://rana.lbl.gov/EisenSoftwareSource.htm. The command-line version of Cluster 3.0 is also covered by this license. * Pycluster is an extension module to the scripting language Python. It is covered by the Python License (same license as Python itself). * Algorithm::Cluster, the interface to the scripting language Perl. It was released under the Artistic License (same license as Perl itself). * The routines in the C Clustering Library can also be used directly by calling them from other C programs. In that case, the Python License applies. . In all cases, copyright notices must be retained in their original form. . The Artistic License is usually distributed in /usr/share/common-licenses/Artistic Files: debian/* Copyright: 2004 Steffen Moeller 2012 Thorsten Alteholz License: GPL-3+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 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 GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-3'. debian/changelog0000644000000000000000000000253012221071541011033 0ustar cluster3 (1.52-2) unstable; urgency=low * add patch from Stefano Rivera (build on armhf) (Closes: #723561) -- Thorsten Alteholz Thu, 26 Sep 2013 18:00:00 +0200 cluster3 (1.52-1) unstable; urgency=low * rebuild needed for motif transition (Closes: #713062) * New upstream release (1.52) * debian/xcluster3.sgml: fix errors * debian/control: canonical vcs-* fields * debin/control: bumped to 3.9.4 (no changes) -- Thorsten Alteholz Mon, 16 Sep 2013 19:00:00 +0200 cluster3 (1.50-1) unstable; urgency=low [ Thorsten Alteholz ] * New upstream release (1.50). * debian/rules: target get-orig-source added [ Steffen Moeller ] * New upstream release (1.40). * Improved on debian/rules. * Finally submitted ITP (Closes: Bug#286167). [ Charles Plessy ] * Initial release. * Manpage built before source package generation, removed docbook-to-man build dependency. -- Thorsten Alteholz Wed, 18 Jul 2012 18:00:00 +0200 cluster3 (1.25-0.2) UNRELEASED; urgency=low * Provides both the motif gui and command line interface. -- Steffen Moeller Tue, 7 Apr 2004 18:31:37 +0200 cluster3 (1.25-0.1) UNRELEASED; urgency=low * Initial Release. -- Steffen Moeller Tue, 6 Apr 2004 18:31:37 +0200 debian/cluster3.sgml0000644000000000000000000001566312125621012011621 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Steffen"> Moeller"> April 6, 2004"> 1"> moeller@pzr.uni-rostock.de"> CLUSTER3"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2003 &dhusername; &dhdate; &dhucpackage; &dhsection; &dhpackage; Eisen-clustering of microarray data &dhpackage; OPTIONS Show summary of options. file loding Allows you to specify a different name for the output files (default is derived from the input file name) Specifies whether to log-transform the data (default is 0, no log-transform) Specifies whether to run k-means clustering instead of hierarchical clustering, and the number of clusters k to use (default: 0) Specifies the horizontal dimension of the SOM grid (default: 2) Specifies the vertical dimension of the SOM grid (default: 1) Specifies whether to calculate an SOM instead of hierarchical clustering (default: 0) Show version of program. -g [0..9] Specifies the distance measure for gene clustering 0: No gene clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman's rank correlation 6: Kendall's tau 7: Euclidean distance 8: Harmonically summed Euclidean distance 9: City-block distance (default: 1) -e [0..9] Specifies the distance measure for microarray clustering 0: No clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman's rank correlation 6: Kendall's tau 7: Euclidean distance 8: Harmonically summed Euclidean distance 9: City-block distance (default: 0) -m [msca] Specifies which hierarchical clustering method to use m: Pairwise complete-linkage s: Pairwise single-linkage c: Pairwise centroid-linkage a: Pairwise average-linkage (default: m) SEE ALSO mapletree (1), smile (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/compat0000644000000000000000000000000212125621012010354 0ustar 9 debian/cluster3.manpages0000644000000000000000000000001312125621012012431 0ustar cluster3.1 debian/cluster3.10000644000000000000000000000544512125621012011014 0ustar .TH "CLUSTER3" "1" .SH "NAME" cluster3 \(em Eisen-clustering of microarray data .SH "SYNOPSIS" .PP \fBcluster3\fR [\fB-f \fIfilename\fR\fP] [\fB-l \fI0|1\fR\fP] [\fB-u \fIjobname\fR\fP] [\fB-g \fI[0..9]\fR\fP] [\fB-e \fI[0..9]\fR\fP] [\fB-m \fI[msca]\fR\fP] [\fB-k \fInumber\fR\fP] [\fB-s \fI0|1\fR\fP] [\fB-x \fInumber\fR\fP] [\fB-y \fInumber\fR\fP] .SH "OPTIONS" .IP "\fB-h\fP\fB\-\-help\fP" 10 Show summary of options. .IP "\fB-f \fIfilename\fR\fP" 10 file loding .IP "\fB-u \fIjobname\fR\fP" 10 Allows you to specify a different name for the output files (default is derived from the input file name) .IP "\fB-l \fI0|1\fR\fP" 10 Specifies whether to log-transform the data (default is 0, no log-transform) .IP "\fB-k \fInumber\fR\fP" 10 Specifies whether to run k-means clustering instead of hierarchical clustering, and the number of clusters k to use (default: 0) .IP "\fB-x \fInumber\fR\fP" 10 Specifies the horizontal dimension of the SOM grid (default: 2) .IP "\fB-y \fInumber\fR\fP" 10 Specifies the vertical dimension of the SOM grid (default: 1) .IP "\fB-s \fI0|1\fR\fP" 10 Specifies whether to calculate an SOM instead of hierarchical clustering (default: 0) .IP "\fB-v\fP \fB\-\-version\fP " 10 Show version of program. .PP \-g [0..9] Specifies the distance measure for gene clustering 0: No gene clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman's rank correlation 6: Kendall's tau 7: Euclidean distance 8: Harmonically summed Euclidean distance 9: City-block distance (default: 1) .PP \-e [0..9] Specifies the distance measure for microarray clustering 0: No clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman's rank correlation 6: Kendall's tau 7: Euclidean distance 8: Harmonically summed Euclidean distance 9: City-block distance (default: 0) .PP \-m [msca] Specifies which hierarchical clustering method to use m: Pairwise complete-linkage s: Pairwise single-linkage c: Pairwise centroid-linkage a: Pairwise average-linkage (default: m) .SH "SEE ALSO" .PP mapletree (1), smile (1). .SH "AUTHOR" .PP This manual page was written by Steffen Moeller moeller@pzr.uni-rostock.de for the \fBDebian\fP system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. .\" created by instant / docbook-to-man, Fri 01 Aug 2008, 13:32 debian/cluster3.doc-base0000644000000000000000000000172412125621012012325 0ustar Document: cluster3 Title: Cluster 3.0 for Windows, Mac OS X, Linux, Unix Author: Michael Eisen; updated by Michiel de Hoon Abstract: This is the manual for Cluster 3.0. Cluster was originally written by Michael Eisen while at Stanford University. We have modified the clustering algorithm in Cluster, and extended the algorithm for Self-Organizing Maps to include two-dimensional rectangular grids. The Euclidean distance and the city-block distance were added as new distance measures between gene expression data. The proprietary Numerical Recipes routines, which were used in the original version of Cluster/TreeView, have been replaced by open source software. . Cluster 3.0 is available for Windows, Mac OS X, Linux, and Unix. Section: Science/Biology Format: PDF Files: /usr/share/doc/cluster3/cluster.pdf.gz /usr/share/doc/cluster3/cluster3.pdf.gz Format: html Index: /usr/share/doc/cluster3/html/index.html Files: /usr/share/doc/cluster3/html/*.html debian/watch0000644000000000000000000000014612125621012010210 0ustar version=3 http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm cluster-(.*)\.tar.gz debian/cluster3-doc.docs0000644000000000000000000000017312125621012012340 0ustar docs/cluster.pdf docs/cluster.texinfo docs/cluster3.pdf docs/cluster3.texinfo docs/structure.eps html/*.html html/images/* debian/xcluster3.sgml0000644000000000000000000000660612213623204012011 0ustar manpage.1'. You may view the manual page with: `docbook-to-man manpage.sgml | nroff -man | less'. A typical entry in a Makefile or Makefile.am is: manpage.1: manpage.sgml docbook-to-man $< > $@ The docbook-to-man binary is found in the docbook-to-man package. Please remember that if you create the nroff version in one of the debian/rules file targets (such as build), you will need to include docbook-to-man in your Build-Depends control field. --> Steffen"> Moeller"> April 6, 2004"> 1"> moeller@pzr.uni-rostock.de"> CLUSTER3"> Debian"> GNU"> GPL"> ]>
&dhemail;
&dhfirstname; &dhsurname; 2003 &dhusername; &dhdate; &dhucpackage; &dhsection; x&dhpackage; Eisen-clustering of microarray data x&dhpackage; DESCRIPTION xcluster3 is the Motif-based X-interface of the Linux-variant of the program cluster by Michael Eisen. It is used to cluster microarray expression data. The presentation of the data is performed by TreeView. This is a Windows program of his, for which the Linux variants TreeView and MapleView exist as Java rewrites. SEE ALSO mapletree (1), treeview (1), smile (1). AUTHOR This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the &gnu; General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. debian/upstream0000644000000000000000000000111512125621012010737 0ustar Contact: M. J. L. de Hoon Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ Name: cluster3 Reference: debian-package: cluster3 author: M. J. L. de Hoon AND S. Imoto AND J. Nolan AND S. Miyano journal: Bioinformatics title: Open Source Clustering Software year: 2004 month: 06 volume: 20 pages: 1453-4 number: 9 DOI: 10.1093/bioinformatics/bth078 PMID: 14871861 url: http://bioinformatics.oxfordjournals.org/content/20/9/1453.long Watch: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm cluster-(.*)\.tar.gz debian/cluster3.docs0000644000000000000000000000002212125621012011566 0ustar NEWS README html/ debian/cluster3.dirs0000644000000000000000000000006212125621012011603 0ustar usr/bin usr/share/doc/cluster3 usr/share/cluster3 debian/menu0000644000000000000000000000017012125621012010043 0ustar ?package(cluster3):needs="X11" section="Applications/Science/Biology" \ title="cluster3" command="/usr/bin/xcluster3" debian/patches/0000755000000000000000000000000012221071652010613 5ustar debian/patches/series0000644000000000000000000000005312220274227012030 0ustar #compile-warnings.patch build-on-arm.patch debian/patches/build-on-arm.patch0000644000000000000000000000064612217030014014120 0ustar Author: Stefano Rivera Description: let pacakage build on armhf --- a/src/Makefile.PL +++ b/src/Makefile.PL @@ -2,10 +2,10 @@ use Config; use POSIX; -# Check if this is a 64 bit machine +# Check if this is an arch where we need position independent code my $CCFLAGS = ''; my $machine = (POSIX::uname())[4]; -if ($machine =~ /64/) { +if ($machine =~ /64|arm/) { $CCFLAGS = '-fPIC'; } debian/patches/compile-warnings.patch0000644000000000000000000000117612125621012015111 0ustar Description: remove compiler warning Index: cluster-1.50/src/command.c =================================================================== --- cluster-1.50.orig/src/command.c 2010-03-28 04:02:14.000000000 +0200 +++ cluster-1.50/src/command.c 2012-07-11 14:37:03.000000000 +0200 @@ -382,7 +382,7 @@ fclose(coordinatefile); fclose(pcfile); if (error) - { printf(error); + { printf("%s",error); free(filename); return; } @@ -403,7 +403,7 @@ fclose(coordinatefile); fclose(pcfile); if (error) - { printf(error); + { printf("%s",error); free(filename); return; } debian/README.Debian0000644000000000000000000000105312125621012011216 0ustar cluster3 for Debian ------------------ The upstream source refers to cluster 1.25 and 3.0 at the same time. Since the original version of Michael Eisen is 2.x, I assume that this should be read as version 1.25 of the 3.0 version of cluster. The executable cluster was renamed to cluster3 in order to avoid name clashes with other packages. The upstream sources compile cluster either as a command line tool or as a motif gui. I decided to name the x-version xcluster3. -- Steffen Moeller , Tue, 6 Apr 2004 18:31:37 +0200 debian/rules0000755000000000000000000001125012215641062010244 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # GNU copyright 1997 to 1999 by Joey Hess. # # Modified to make a template file for a multi-binary package with separated # build-arch and build-indep targets by Bill Allombert 2001 # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # This has to be exported to make some magic below work. export DH_OPTIONS # These are used for cross-compiling and for saving the configure script # from having to guess our platform (since we know it already) DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) CFLAGS += -Wall -g -fPIC ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) INSTALL_PROGRAM += -s endif #Architecture configure: configure-stamp configure-stamp: cp -f /usr/share/misc/config.sub config.sub cp -f /usr/share/misc/config.guess config.guess touch configure-stamp build-arch: build-arch-stamp-nox build-arch-clean build-arch-stamp-x cluster3.1 xcluster3.1 build-arch-stamp-nox: configure # Add here commands to compile the arch part of the package. CFLAGS="$(CFLAGS)" ./configure -C --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info --without-x $(MAKE) CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" cp src/cluster cluster.nox touch build-arch-stamp-nox build-arch-stamp-x: configure CFLAGS="$(CFLAGS)" ./configure -C --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info --with-x $(MAKE) CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" cp src/cluster cluster.x touch build-arch-stamp-x # in order to build build-arch-stamp-x after build-arch-stamp-nox # any object file needs to be cleaned build-arch-clean: configure $(MAKE) clean install-arch-perl: install-arch-perl-stamp install-arch-perl-stamp: #error with prefix defined: perl Makefile.PL prefix=$(CURDIR)/debian/cluster3/usr/ perl Makefile.PL INSTALL_BASE=$(CURDIR)/debian/cluster3/usr/ make make test make install cluster3.1: debian/cluster3.sgml docbook-to-man $< > $@ xcluster3.1: debian/xcluster3.sgml docbook-to-man $< > $@ build-indep: build-indep-stamp build-indep-stamp: # Add here commands to compile the indep part of the package. touch build-indep-stamp clean: dh_testdir dh_testroot rm -f build-arch-stamp* build-indep-stamp #CONFIGURE-STAMP# # Add here commands to clean up after the build process. [ ! -f Makefile ] || $(MAKE) clean -find . -name .deps -a -type d | xargs rm -rf dh_clean config.status config.cache config.sub config.guess src/*.o X11/*.o src/cluster X11/cluster cluster3.1 xcluster3.1 src/Makefile src/Makefile.old X11/Makefile Makefile install: install-indep install-arch install-indep: dh_testdir -i dh_testroot -i dh_prep -i dh_installdirs -i # Add here commands to install the indep part of the package into # debian/-doc. #INSTALLDOC# dh_install -i install-arch: build-arch install-arch-perl dh_testdir -a dh_testroot -a dh_prep -a dh_installdirs -a # Add here commands to install the arch part of the package into # debian/tmp. cp cluster.x $(CURDIR)/debian/cluster3/usr/bin/xcluster3 cp cluster.nox $(CURDIR)/debian/cluster3/usr/bin/cluster3 cp doc/* $(CURDIR)/debian/cluster3/usr/share/doc/cluster3 cp -r example $(CURDIR)/debian/cluster3/usr/share/cluster3 dh_install -s # Must not depend on anything. This is to be called by # binary-arch/binary-indep # in another 'make' thread. binary-common: dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installmenu dh_installman cluster3.1 xcluster3.1 dh_link dh_strip dh_compress dh_fixperms dh_perl # dh_python dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb # Build architecture independant packages using the common target. binary-indep: build-indep install-indep $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common # Build architecture dependant packages using the common target. binary-arch: build-arch install-arch $(MAKE) -f debian/rules DH_OPTIONS=-a binary-common binary: binary-arch .PHONY: build build-arch clean binary-indep binary-arch binary install install-indep install-arch get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/source/0000755000000000000000000000000012221071652010464 5ustar debian/source/format0000644000000000000000000000001412125621012011664 0ustar 3.0 (quilt)