complearn 0.6.2

data/doc/man/maketree.1

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+.TH MAKETREE 1
+.SH NAME
+maketree \- perform Quartet Tree Reconstruction on a distance matrix to produce an unrooted binary tree
+.SH SYNOPSIS
+.B maketree [-h] [-f
+.I configfile
+.B ]
+.I matrix.txt treeout.dot
+.SH DESCRIPTION
+.B maketree
+tries to find an optimal tree to represent an input distance matrix \fBmatrix.txt\fR.
+It uses the Quartet Tree Reconstruction method.  The program starts with a random tree, and continues to try small modifications to improve the tree score.  Eventually, the tree will stop easily improving.  The algorithm will then write the best tree it found to \fBtreeout.dot\fR.  This is a \fB.dot\fR-format file,
+which means that it can be used with the \fBgraphviz\fR package tools such as \fBdot (1)\fR or \fBneato (1)\fR.  The external nodes are labelled with integers starting with 0.  This file may be relabelled using the \fBlabeltree (1)\fR utility if it is to be laid out for human interpretation.
+
+The following configuration variables are relevant to this algorithm:
+
+.BR UnpairedPenalty
+a floating-point number representing the penalty associated with leaves that do not cluster adjacent to other leaves.  A value of 0, the default, means no penalty.  A value above 0 (typically 0.05-0.3) indicates an additional cost associated with each of these "unpaired" nodes.  Some types of distance matrices, particularly inconsistent ones, can often lead to degenerate trees that are linear and heavily imbalanced without this penalty.
+
+.BR UseBestThirdOnly
+a boolean value indicating if the quartet tree evaluation function should
+restrict its calculations to only include the single best quartet out of every triple of quartets associated with each group of four labels.  This option is off by default.  If activated, it may speed up searches but may also lead to different results.
+
+.BR TreesPerTry
+an integer specifying the number of mutated trees to try per failure-counter increment.  Default 1000.
+
+.BR MaxFailedTries
+an integer specifying how many failed batches of trees must occur in succession before the program exits.  Default 10.
+
+Input files for this program can be created by \fBncdmatrix (1)\fR.  The NCD is 
+defined in
+.BR ncd(1).
+
+For more information on the details of this algorithm, please see
+\fIAlgorithmic Clustering of Music\fR by \fBCilibrasi, Vitanyi,\fR and \fBde Wolf\fR at \fBhttp://www.arxiv.org/abs/cs.SD/0303025\fR
+.SH OPTIONS
+.IP -h
+Print usage information and exit.
+.IP "-f configfile"
+Use a different configuration file than the default search locations
+.SH FILES
+.I $HOME/.complearnrc
+.RS per-user configuration file, overrides systemwide default
+.I /etc/complearnrc
+.RS the systemwide configuration file
+see
+.BR complearn (5)
+for further details.
+.SH ENVIRONMENT
+none
+.SH DIAGNOSTICS
+If any of the files cannot be read, an error will be printed and the program exits with a nonzero exit code.
+.SH "SEE ALSO"
+.BR ncdmatrix (1),
+.BR labeltree (1),
+.BR makesvm (1),
+.BR complearn (5),
+.BR ncd (1)

data/doc/man/ncd.1

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+.TH NCD 1
+.SH NAME
+ncd \- compute the Normalized Compression Distance between two files
+.SH SYNOPSIS
+.B ncd [-h] [-f
+.I configfile
+.B ]
+.I file1 file2
+.SH DESCRIPTION
+.B ncd
+computes the Normalized Compression Distance between two files, which
+is defined as
+.TP
+.B NCD(a,b) = (C(a,b) - min(C(a),C(b))) / max(C(a),C(b))
+.TP
+.B where 
+.TP
+.B C(a,b) means "the compressed size of the concatenation of a and b"
+.TP
+.B C(a) means "the compressed size of a"
+.TP
+.B C(b) means "the compressed size of b"
+.B ncd
+will print a non-negative number 0 <= x < 1.1 representing how different the two files are.
+Smaller numbers represent more similar files.  The largest number is somewhere near
+1.  It is not exactly 1 due to imperfections in compression techniques, but for most
+standard compression algorithms you are unlikely to see a number above 1.1 in any case.
+Two compressors are available by default: bzip2 and gzip.  These may be selected with
+an option in the \fB.complearnrc\fR, see \fBcomplearn (5)\fR for more details.
+.SH OPTIONS
+.IP -h
+Print usage information and exit.
+.IP "-f configfile"
+Use a different configuration file than the default search locations
+.SH FILES
+.I $HOME/.complearnrc
+.RS per-user configuration file, overrides systemwide default
+.I /etc/complearnrc
+.RS the systemwide configuration file
+see
+.BR complearn (5)
+for further details.
+.SH ENVIRONMENT
+none
+.SH DIAGNOSTICS
+If either of the two files cannot be read, an error will be printed and the program exits with a
+nonzero exit code.
+.SH "SEE ALSO"
+.BR ncdvector (1),
+.BR ncdmatrix (1),
+.BR complearn (5)

data/doc/man/ncdmatrix.1

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+.TH NCDMATRIX 1
+.SH NAME
+ncdmatrix \- compute the Normalized Compression Distance for a group of files to create a distance matrix
+.SH SYNOPSIS
+.B ncdmatrix [-h] [-f
+.I configfile
+.B ]
+.I [ filelist | dirname ]
+.SH DESCRIPTION
+.B ncdmatrix
+computes the Normalized Compression Distance between all pairs of files in a
+group.  If a filelist is used, filenames must be specified one per line.  If a directory name is used, all files in that directory (non-recursively) will
+be used in sorted order.  For a group of \fBn \fRfiles, there will be \fBn*n\fR different numbers printed.  There will be \fBn\fR positive real numbers printed on each line, separated by spaces.  There will be \fBn\fR of these lines printed.
+
+The NCD is defined in
+.BR ncd(1).
+The resultant NCD matrix is suitable for other learning applications such as Quartet Tree Reconstruction (\fBmaketree (1)\fR) or as a Support Vector Machine Kernel Matrix.
+.SH OPTIONS
+.IP -h
+Print usage information and exit.
+.IP "-f configfile"
+Use a different configuration file than the default search locations
+.SH FILES
+.I $HOME/.complearnrc
+.RS per-user configuration file, overrides systemwide default
+.I /etc/complearnrc
+.RS the systemwide configuration file
+see
+.BR complearn (5)
+for further details.
+.SH ENVIRONMENT
+none
+.SH DIAGNOSTICS
+If any of the files cannot be read, an error will be printed and the program exits with a nonzero exit code.
+.SH "SEE ALSO"
+.BR ncd (1),
+.BR maketree (1),
+.BR ncdvector (1),
+.BR makesvm (1),
+.BR complearn (5)

data/doc/man/ncdvector.1

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+.TH NCDVECTOR 1
+.SH NAME
+ncdvector \- compute the Normalized Compression Distance between a file and a list of files to create a vector
+.SH SYNOPSIS
+.B ncdvector [-h] [-f
+.I configfile
+.B ]
+.I testfile featurelist
+.SH DESCRIPTION
+.B ncdvector
+computes the Normalized Compression Distance between testfile and
+each of the files listed in
+.B featurelist.
+The NCD is defined in
+.BR ncd(1).
+The result will be printed as a single line of nonnegative real numbers separated by spaces.  If a directory is given, the files will be sorted in alphabetical order.  The NCD will be calculated first between testfile and the first listed file in 
+.B featurelist,
+and this number will be printed.  Then, the NCD will be calculated between testfile and the second to obtain the second number.  This continues for all files in
+.B filelist.
+The resultant vector is a dimensionality-reduced projection of the original file suitable for use in other machine-learning techniques such as Support Vector Machines.
+.SH OPTIONS
+.IP -h
+Print usage information and exit.
+.IP "-f configfile"
+Use a different configuration file than the default search locations
+.SH FILES
+.I $HOME/.complearnrc
+.RS per-user configuration file, overrides systemwide default
+.I /etc/complearnrc
+.RS the systemwide configuration file
+see
+.BR complearn (5)
+for further details.
+.SH ENVIRONMENT
+none
+.SH DIAGNOSTICS
+If any of the files cannot be read, an error will be printed and the program exits with a nonzero exit code.
+.SH "SEE ALSO"
+.BR ncd (1),
+.BR makesvm (1),
+.BR ncdmatrix (1),
+.BR complearn (5)

data/doc/readme.txt

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+CompLearn
+
+A compression-based data-mining toolkit by Rudi Cilibrasi (cilibrar@ofb.net)
+--------------------------------------------------------------------------
+
+The CompLearn Toolkit enables you to do data mining using data compression.
+It also allows you to do Quartet Tree Reconstruction as well as
+Support Vector Machine experiments with these techniques.  Using this
+package, you can do powerful pattern recognition easily from your
+shell command line using a simple suite of tools.  Applications include
+music cateogrization, text classification, handwritten digit recognition,
+and evolutionary tree reconstruction.  The technique is based on a
+very general theoretical notion of Kolmogorov Complexity, and so is
+undoubtedly applicable to many as yet unknown disciplines.
+
+Please look at the manual pages for
+
+maketree.1
+labeltree.1
+
+ncd.1
+ncdmatrix.1
+ncdvector.1
+
+makesvm.1
+
+complearn.5
+
+
+In order to make full use this package, you should have the following
+software installed:
+
+1) ruby-1.8.0 from http://www.ruby-lang.org/en/20020102.html
+
+at least one but ideally both of the following compressors:
+2) ruby bz2 library from ftp://moulon.inra.fr/pub/ruby/bz2.tar.gz
+and
+2) the ruby zlib (gzip) library, often included with ruby-1.8.0
+under Debian it is the package libzlib-ruby1.8
+
+3) the AT&T "graphviz" package at http://www.research.att.com/sw/tools/graphviz
+
+Debian users may also need the ruby1.8, ruby1.8-dev, and libruby1.8 packages
+
+Please note that graphviz is only necessary to convert trees to postscript
+layouts for human interpretation.
+
+To compile this package, first type
+
+./configure
+
+in the top level directory.  Next,
+
+cd ext/
+make
+
+to create the extension module, CompLearn.so
+
+Now, the installation part must be done as root; starting from the ext/ dir,
+su
+(type your root password here)
+make install
+cd ..
+(this should take you to the top-level of the distribution directory)
+make install
+exit
+(leave the root shell)
+
+If you like, you can now run some tests, or just try to follow the example
+in doc/example.txt
+
+Now go back to the top level distribution directory and make sure the
+built-in tests work, if you have the Ruby Unit Testing library installed
+
+cd ..
+ruby tests/tests.rb
+
+--------------------------------------------------------------------------
+This section will only be necessary for users that must install to
+nonstandard locations or for other reasons have a complicated situation.
+
+In order to use this extension, you must add the directory containing
+CompLearn.so to your RUBYLIB environment variable search path.
+Also, you must put
+require 'CompLearn'
+in your ruby source.
+
+The TreeScore class will be defined when you use this module.
+
+PARALLEL MODE OF EXECUTION
+--------------------------------------------------------------------------
+To run this program, first make sure you have ssh-agent running.
+Then, do an ssh-add for the key that will be used to start the parallel
+processes.
+
+Finally, do, for example:
+
+ruby parstart tests/ncdTest.rb
+
+Make sure your PATH, LD_LIBRARY_PATH, and RUBYLIB are set correctly.
+

data/doc/userguide.txt

@@ -0,0 +1,46 @@
+CompLearn
+
+A compression-based data-mining toolkit by Rudi Cilibrasi (cilibrar@ofb.net)
+--------------------------------------------------------------------------
+
+Please see the manual pages:
+ncd (1), ncdvector (1),  ncdmatrix (1), maketree (1), makesvm (1),
+labeltree(1), and complearn(5)
+
+Here are short descriptions of what each command can do:
+--------------------------------------------------------------------------
+
+ncd <file1> <file2>
+
+computes the Normalized Compression Distance between two files
+specified on the command line.
+
+Theoretically, this number is supposed to be between 0 and 1, but
+in practical terms, we sometimes see values as high as about 1.1.
+
+ncdvector <file1> {filelist.txt|dirname}
+
+computes a list of ncd's according to files listed in filelist.txt or
+all files in the directory dirname.  in filelist.txt, each line should
+be a filename
+
+ncdmatrix {filelist.txt|dirname}
+
+computes a square distance matrix of all pairs of files specified
+as a list of files or in a directory.
+
+maketree test.dm tree.dot
+
+computes a best-fitting unrooted binary tree from a given distance matrix.
+The distance matrix should be the output of the ncdmatrix command.  The
+result is put in a file called tree.dot in this example.
+
+labeltree tree.dot {filelist.txt|dirname}
+
+labels a tree's leaves according to a group of files.  This is best
+used before layout with dot or neato.
+
+makesvm categoryfile.txt
+
+create a pair of trainsvm.txt and testsvm.txt files for SVM experimentation.
+

data/examples/genes/blueWhale.txt

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                                     

data/examples/genes/cat.txt

@@ -0,0 +1 @@
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data/examples/genes/chimpanzee.txt

@@ -0,0 +1 @@
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                                                        

data/examples/genes/finWhale.txt

@@ -0,0 +1 @@
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                                         

data/examples/genes/graySeal.txt

@@ -0,0 +1 @@
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  

data/examples/genes/harborSeal.txt

@@ -0,0 +1 @@
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                                 

data/examples/genes/horse.txt

@@ -0,0 +1 @@
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atggtacttcctgtttgcctacgccatcctacgctccattcccaacaaactaggcggcgtattagccctaatcctctccatcctgatcctagcactcatccccaccctccacatatcaaaacaacgaagcataatattccggcctctcagccaatgcgtattctgactcttagtggcagacttactgacactaacatgaatcggcggacagccagtggaacacccatacgtaattatcggccaactggcctcaatcctctacttctccctaattctcatttttataccactcgcaagcaccatcgaaaacaatcttctaaaatgaagagtccctgtagtatatcgcacattaccctggtcttgtaaaccagaaaagggggaaaacgtttcctcccaaggactatcaaggaagaagctctagctccaccatcaacacccaaagctgaaattctacttaaactattccttgatttcttcccctaaacgacaacaatttaccctcatgtgctatgtcagtatcagattatacccccacataacaccatacccacctgacatgcaatatcttatgaatggcctatgtacgtcgtgcattaaattgtctgccccatgaataataagcatgtacataatatcatttatcttacataagtacattatattattgatcgtgcataccccatccaagtcaaatcatttccagtcaacacgcatatcacagcccatgttccacgagcttaatcaccaagccgcgggaaatcagcaaccctcccaactacgtgtcccaatcctcgctccgggcccatccaaacgtgggggtttctacaatgaaactatacctggcatctggttctttcttcagggccattcccacccaacctcgcccattctttccccttaaataagacatctcgatggactaatgactaatcagcccatgctcacacataactgtgatttcatgcatttggtatctttttatatttggggatgctatgactcagctatggccgtcaaaggcctcgacgcagtcaattaaattgaagctggacttaaattgaacgttattcctccgcatcagcaaccataaggtgttattcagtccatggtagcgggacataggaaacaagtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctacccgcgcagtaagcaagtaatatagctttcttaatcaaaccccccctaccccccattaaactccacatatgtacattcaacacaatcttgccaaaccccaaaaacaagactaaacaatgcacaatacttcatgaagcttaaccctcgcatgccaaccataataactcaacacacctaacaatcttaacagaactttccccccgccattaataccaacatgctactttaatcaataaaatttccatagacaggcatccccctagatctaattttctaaatctgtcaacccttcttccccc                    

data/examples/genes/human.txt

@@ -0,0 +1 @@
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                                                  

data/examples/genes/mouse.txt

@@ -0,0 +1 @@
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                        

data/examples/genes/rat.txt

@@ -0,0 +1 @@
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                   

data/ext/Makefile

@@ -0,0 +1,167 @@
+
+SHELL = /bin/sh
+
+#### Start of system configuration section. ####
+
+srcdir = .
+topdir = /usr/lib/ruby/1.8/i386-linux
+hdrdir = $(topdir)
+VPATH = $(srcdir)
+prefix = $(DESTDIR)/usr
+exec_prefix = $(prefix)
+sitedir = $(prefix)/local/lib/site_ruby
+rubylibdir = $(libdir)/ruby/$(ruby_version)
+builddir = $(ac_builddir)
+archdir = $(rubylibdir)/$(arch)
+sbindir = $(exec_prefix)/sbin
+compile_dir = $(DESTDIR)/tmp/ruby1.8-1.8.1+1.8.2pre2/build-tree/ruby-1.8.2
+datadir = $(prefix)/share
+includedir = $(prefix)/include
+infodir = $(prefix)/info
+top_builddir = $(ac_top_builddir)
+sysconfdir = $(DESTDIR)/etc
+mandir = $(datadir)/man
+libdir = $(exec_prefix)/lib
+sharedstatedir = $(prefix)/com
+oldincludedir = $(DESTDIR)/usr/include
+sitearchdir = $(sitelibdir)/$(sitearch)
+bindir = $(exec_prefix)/bin
+localstatedir = $(DESTDIR)/var
+sitelibdir = $(sitedir)/$(ruby_version)
+libexecdir = $(exec_prefix)/libexec
+
+CC = gcc
+LIBRUBY = $(LIBRUBY_SO)
+LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
+LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
+LIBRUBYARG_STATIC = -l$(RUBY_SO_NAME)-static
+
+CFLAGS   =  -fPIC -Wall -g -O2  -fPIC 
+CPPFLAGS = -I. -I$(topdir) -I$(hdrdir) -I$(srcdir)  
+CXXFLAGS = $(CFLAGS) 
+DLDFLAGS =   
+LDSHARED = gcc -shared
+AR = ar
+EXEEXT = 
+
+RUBY_INSTALL_NAME = ruby1.8
+RUBY_SO_NAME = $(RUBY_INSTALL_NAME)
+arch = i386-linux
+sitearch = i386-linux
+ruby_version = 1.8
+ruby = /usr/bin/ruby1.8
+RUBY = $(ruby)
+RM = $(RUBY) -run -e rm -- -f
+MAKEDIRS = $(RUBY) -run -e mkdir -- -p
+INSTALL_PROG = $(RUBY) -run -e install -- -vpm 0755
+INSTALL_DATA = $(RUBY) -run -e install -- -vpm 0644
+
+#### End of system configuration section. ####
+
+
+LIBPATH =  -L"$(libdir)"
+DEFFILE = 
+
+CLEANFILES = 
+DISTCLEANFILES = 
+
+target_prefix = 
+LOCAL_LIBS = 
+LIBS = $(LIBRUBYARG_SHARED)  -lpthread -ldl -lcrypt -lm   -lc
+OBJS = Quartet.o TreeScore.o
+TARGET = CompLearn
+DLLIB = $(TARGET).so
+STATIC_LIB = $(TARGET).a
+
+RUBYCOMMONDIR = $(sitedir)$(target_prefix)
+RUBYLIBDIR    = $(sitelibdir)$(target_prefix)
+RUBYARCHDIR   = $(sitearchdir)$(target_prefix)
+
+CLEANLIBS     = "$(TARGET).{lib,exp,il?,tds,map}" $(DLLIB)
+CLEANOBJS     = "*.{o,a,s[ol],pdb,bak}"
+
+all:		$(DLLIB)
+static:		$(STATIC_LIB)
+
+clean:
+		@$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
+
+distclean:	clean
+		@$(RM) Makefile extconf.h conftest.* mkmf.log
+		@$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
+
+realclean:	distclean
+install: $(RUBYARCHDIR)
+install: $(RUBYARCHDIR)/$(DLLIB)
+$(RUBYARCHDIR)/$(DLLIB): $(DLLIB) $(RUBYARCHDIR)
+	@$(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
+install: $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/CompressionObject.rb
+$(RUBYLIBDIR)/CompLearnLib/CompressionObject.rb: $(srcdir)/lib/CompLearnLib/CompressionObject.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/CompressionObject.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/CompressionTask.rb
+$(RUBYLIBDIR)/CompLearnLib/CompressionTask.rb: $(srcdir)/lib/CompLearnLib/CompressionTask.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/CompressionTask.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/FoundComp.rb
+$(RUBYLIBDIR)/CompLearnLib/FoundComp.rb: $(srcdir)/lib/CompLearnLib/FoundComp.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/FoundComp.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/DistMatrix.rb
+$(RUBYLIBDIR)/CompLearnLib/DistMatrix.rb: $(srcdir)/lib/CompLearnLib/DistMatrix.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/DistMatrix.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/Ncd.rb
+$(RUBYLIBDIR)/CompLearnLib/Ncd.rb: $(srcdir)/lib/CompLearnLib/Ncd.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/Ncd.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/RunEnv.rb
+$(RUBYLIBDIR)/CompLearnLib/RunEnv.rb: $(srcdir)/lib/CompLearnLib/RunEnv.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/RunEnv.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/Task.rb
+$(RUBYLIBDIR)/CompLearnLib/Task.rb: $(srcdir)/lib/CompLearnLib/Task.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/Task.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/TaskMaster.rb
+$(RUBYLIBDIR)/CompLearnLib/TaskMaster.rb: $(srcdir)/lib/CompLearnLib/TaskMaster.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/TaskMaster.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/TaskMasterMPI.rb
+$(RUBYLIBDIR)/CompLearnLib/TaskMasterMPI.rb: $(srcdir)/lib/CompLearnLib/TaskMasterMPI.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/TaskMasterMPI.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/TaskMasterSingle.rb
+$(RUBYLIBDIR)/CompLearnLib/TaskMasterSingle.rb: $(srcdir)/lib/CompLearnLib/TaskMasterSingle.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/TaskMasterSingle.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/Tree.rb
+$(RUBYLIBDIR)/CompLearnLib/Tree.rb: $(srcdir)/lib/CompLearnLib/Tree.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/Tree.rb $(RUBYLIBDIR)/CompLearnLib
+install: $(RUBYLIBDIR)/CompLearnLib/CLConfig.rb
+$(RUBYLIBDIR)/CompLearnLib/CLConfig.rb: $(srcdir)/lib/CompLearnLib/CLConfig.rb $(RUBYLIBDIR)/CompLearnLib
+	@$(INSTALL_DATA) $(srcdir)/lib/CompLearnLib/CLConfig.rb $(RUBYLIBDIR)/CompLearnLib
+$(RUBYARCHDIR):
+	@$(MAKEDIRS) $(RUBYARCHDIR)
+$(RUBYLIBDIR)/CompLearnLib:
+	@$(MAKEDIRS) $(RUBYLIBDIR)/CompLearnLib
+
+site-install: install
+
+.SUFFIXES: .c .cc .m .cxx .cpp .C .o
+
+.cc.o:
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c $<
+
+.cpp.o:
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c $<
+
+.cxx.o:
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c $<
+
+.C.o:
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c $<
+
+.c.o:
+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
+
+$(DLLIB): $(OBJS)
+	@-$(RM) $@
+	$(LDSHARED) $(DLDFLAGS) $(LIBPATH) -o $(DLLIB) $(OBJS) $(LOCAL_LIBS) $(LIBS)
+
+$(STATIC_LIB): $(OBJS)
+	$(AR) cru $@ $(OBJS)
+	@-ranlib $(DLLIB) 2> /dev/null || true
+
+distdir: