diff --git a/Makefile.m4 b/Makefile.m4
new file mode 100644
index 0000000..b2b9f04
--- /dev/null
+++ b/Makefile.m4
@@ -0,0 +1,30 @@
+PREFIX=M4_PREFIX
+BIN_DIR=M4_BINDIR
+DATA_DIR=M4_DATADIR
+PY_DIR=M4_PYDIR
+DOC_DIR=M4_DOCDIR
+
+SCRIPTS_DIR=${DATA_DIR}/laydi/scripts/
+
+install: install_laydi install_doc
+
+install_laydi:
+	## Install binary files		
+	install -m 755 -D bin/fluents ${BIN_DIR}/fluents
+	install -m 755 -D bin/dataset ${BIN_DIR}/dataset
+	
+	## Install library files
+	find fluents/ -type f -name '*.py' -exec install -m 644 -D {} ${PY_DIR}/{} \;
+	find fluents/ -type f -name '*.glade' -exec install -m 644 -D {} ${PY_DIR}/{} \;
+	
+	## Install icons
+	find icons/ -type f -name '*.png' -exec install -m 644 -D {} ${DATA_DIR}/{} \;
+
+install_scripts:
+	find scripts/ -type f -exec install -D {} ${SCRIPTS_DIR}/{} \;
+
+install_doc:
+	DOC_DIR=${DOC_DIR}/ make -C doc install
+	install -m 644 README ${DOC_DIR}/
+	install -m 644 LICENSE ${DOC_DIR}/
+
diff --git a/bin/fluents b/bin/fluents
index 7bda116..3e122f8 100755
--- a/bin/fluents
+++ b/bin/fluents
@@ -5,7 +5,8 @@ import os
 import sys
 from fluents import fluents, project, workflow, main
 #import workflows
-import cfgparse, optparse
+from fluents import cfgparse
+import optparse
 
 PROGRAM_NAME = 'fluents'
 VERSION = '0.1.0'
@@ -60,6 +61,10 @@ if __name__ == '__main__':
     options, params = parse_options()
     main.options = options
     
+    for dir in main.options.workflowdir.split(';'):
+        if dir.strip() != "" and os.path.exists(dir):
+            sys.path.append(dir)
+
     if options.list_workflows:
         list_workflows()
         sys.exit(0)
diff --git a/configure b/configure
new file mode 100755
index 0000000..c66407e
--- /dev/null
+++ b/configure
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+
+TEMP=`getopt -o "" --long prefix:,bindir:,datadir:,pydir: \
+     -n 'configure' -- "$@"`
+
+eval set -- "$TEMP"
+
+while true ; do
+	case "$1" in
+		--prefix) PREFIX=$2 ; shift 2 ;;
+		--bindir) BINDIR=$2 ; shift 2 ;;
+		--datadir) DATADIR=$2 ; shift 2 ;;
+		--pydir) PYDIR=$2 ; shift 2 ;;
+		--) shift ; break ;;
+		*) echo "Internal error!" ; exit 1 ;;
+	esac
+done
+
+if [[ $PREFIX == "" ]] ; then PREFIX=/usr/local ; fi
+if [[ $BINDIR == "" ]] ; then BINDIR=$PREFIX/bin ; fi
+if [[ $DATADIR == "" ]] ; then DATADIR=$PREFIX/share/laydi ; fi
+if [[ $DOCDIR == "" ]] ; then DOCDIR=$PREFIX/share/doc/laydi; fi
+if [[ $PYDIR == "" ]] ; then PYDIR=$PREFIX/share/python-support/laydi; fi
+
+m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \
+   -D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \
+   -D M4_PYDIR=$PYDIR Makefile.m4 > Makefile
+
+m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \
+   -D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \
+   -D M4_PYDIR=$PYDIR doc/Makefile.m4 > doc/Makefile
+
+m4 -D M4_PREFIX=$PREFIX -D M4_BINDIR=$BINDIR \
+   -D M4_DATADIR=$DATADIR -D M4_DOCDIR=$DOCDIR \
+   -D M4_PYDIR=$PYDIR fluents/paths.py.m4 > fluents/paths.py
+
diff --git a/debian/rules b/debian/rules
index 67780d5..164ed0c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,22 +13,21 @@ CFLAGS = -Wall -g
 PYVERS=$(shell pyversions -vs)
 
 configure: configure-stamp
+
 configure-stamp:
 	dh_testdir
-	
 	touch configure-stamp
 
 build: $(PYVERS:%=build-python%)
 
 build-python%:
 	dh_testdir
-	python$* setup.py build
+#	python$* setup.py build
 	touch $@
 
 clean: 
 	# Add here commands to clean up after the build process.
 	-rm -r build
-
 	dh_clean 
 
 install: build $(PYVERS:%=install-python%)
@@ -37,8 +36,10 @@ install-python%:
 	dh_testroot
 	dh_clean -k 
 	dh_installdirs
-
-	python$* setup.py install --root=$(CURDIR)/debian/fluents --install-data=/usr/share/fluents
+	./configure --prefix ${CURDIR}/debian/fluents/usr
+	sed -i 's:${CURDIR}/debian/fluents::' fluents/paths.py
+	make install
+#	python$* setup.py install --root=$(CURDIR)/debian/fluents --install-data=/usr/share/fluents
 
 	# Remove all *.pyc files, created in the postinst
 #	find $(CURDIR)/debian/python-networkx -name "*.pyc" -exec rm {} ';'
@@ -46,8 +47,9 @@ install-python%:
 
 # Build architecture-independent files here.
 binary-indep: build install
-	mkdir -p $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html
-	epydoc --html -o $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html fluents
+	make -C doc install
+#	mkdir -p $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html
+#	epydoc --html -o $(CURDIR)/debian/fluents-doc/usr/share/doc/fluents-doc/html fluents
 
 # Build architecture-dependent files here.
 binary-arch: build install
@@ -70,4 +72,4 @@ binary-arch: build install
 	dh_builddeb
 
 binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+.PHONY:  build clean binary-indep binary-arch binary install configure
diff --git a/doc/Makefile b/doc/Makefile
index 6dbf8ad..aca46da 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,4 +1,6 @@
 
+DOC_DIR=/home/einarr/src/fluents-8/debian/fluents/usr/share/doc/laydi
+
 all: html
 
 html:
@@ -8,7 +10,11 @@ html:
 	@echo ----------------
 	epydoc --html --inheritance listed -o html/ ../fluents 2> epydoc-html.log
 
+install:
+	find html/ -type f -exec install -m 644 -D '{}' ${DOC_DIR}/'{}' \;
+
 clean:
 	-rm -rf html
 	-rm epydoc-html.log
 
+	
diff --git a/doc/Makefile.m4 b/doc/Makefile.m4
new file mode 100644
index 0000000..6946e8d
--- /dev/null
+++ b/doc/Makefile.m4
@@ -0,0 +1,20 @@
+
+DOC_DIR=M4_DOCDIR
+
+all: html
+
+html:
+	@echo ----------------
+	@echo Generating epydoc html code documentation.
+	@echo See epydoc-html.log for epydoc log.
+	@echo ----------------
+	epydoc --html --inheritance listed -o html/ ../fluents 2> epydoc-html.log
+
+install:
+	find html/ -type f -exec install -m 644 -D '{}' ${DOC_DIR}/'{}' \;
+
+clean:
+	-rm -rf html
+	-rm epydoc-html.log
+
+	
diff --git a/cfgparse.py b/fluents/cfgparse.py
similarity index 100%
rename from cfgparse.py
rename to fluents/cfgparse.py
diff --git a/fluents/fluents.py b/fluents/fluents.py
index 3e10d56..7d0b893 100644
--- a/fluents/fluents.py
+++ b/fluents/fluents.py
@@ -19,9 +19,10 @@ from logger import logger, LogView
 
 PROGRAM_NAME = 'fluents'
 VERSION = '0.1.0'
-DATADIR = os.path.dirname(sys.modules['fluents'].__file__)
-ICONDIR = os.path.join(DATADIR,"..","icons")
-GLADEFILENAME = os.path.join(DATADIR, 'fluents.glade')
+DATADIR = os.path.join(main.PYDIR, 'fluents')
+#ICONDIR = os.path.join(DATADIR,"..","icons")
+ICONDIR = main.ICONDIR
+GLADEFILENAME = os.path.join(main.PYDIR, 'fluents/fluents.glade')
 _icon_mapper = {dataset.Dataset: 'dataset',
                dataset.CategoryDataset: 'category_dataset',
                dataset.GraphDataset: 'graph_dataset',
diff --git a/fluents/main.py b/fluents/main.py
index 9ed81ef..ca61570 100644
--- a/fluents/main.py
+++ b/fluents/main.py
@@ -1,5 +1,16 @@
     
 import sys
+import os.path
+import paths
+
+# Site specific directories set by configure script.
+PREFIX = paths.PREFIX
+BINDIR = paths.BINDIR
+DATADIR = paths.DATADIR
+DOCDIR = paths.DOCDIR
+PYDIR = paths.PYDIR
+
+ICONDIR = os.path.join(DATADIR, 'icons')
 
 #: Dictionary of observers
 _observers = {}
diff --git a/fluents/paths.py.m4 b/fluents/paths.py.m4
new file mode 100644
index 0000000..0a8c799
--- /dev/null
+++ b/fluents/paths.py.m4
@@ -0,0 +1,7 @@
+
+PREFIX = "M4_PREFIX"
+BINDIR = "M4_BINDIR"
+DATADIR = "M4_DATADIR"
+DOCDIR = "M4_DOCDIR"
+PYDIR = "M4_PYDIR"
+
diff --git a/fluents/workflow.py b/fluents/workflow.py
index bb42cbc..6777fcb 100644
--- a/fluents/workflow.py
+++ b/fluents/workflow.py
@@ -6,12 +6,11 @@ import logger
 import fluents
 import main
 
-def _workflow_classes(modname):
+def _workflow_classes(dir, modname):
     """Returns a list of all subclasses of Workflow in a given module"""
     workflow_classes = []
 
-    __import__('workflows.%s' % modname)
-    module = sys.modules['workflows.%s' % modname]
+    module = __import__('%s' % (modname,))
 
     d = module.__dict__
     for wf in d.values():
@@ -58,7 +57,7 @@ def find_workflow(basename):
         fn = os.path.join(dir, "%s.py" % basename)
         if os.path.isfile(fn):
             wf_file = fn
-            return _workflow_classes(basename)[0]
+            return _workflow_classes(dir, basename)[0]
 
     return None