diff --git a/README b/README
index 72193b94e370cb6ff29d53ab22d43a6e7eb217fb..3f019a0c0699cc90171f9dc3030307146fd932de 100644
--- a/README
+++ b/README
@@ -57,6 +57,7 @@ Todo:
 * Create a web interface url to watch the progress of a batch job.
 * Use virtualenv?
 * Perhaps the WSGI file should be somewhere else and be called mutalyzer.wsgi?
+* Password for MySQL user.
 
 
 Notes for server setup (Europium VM copy):
diff --git a/bin/mutalyzer-batchd b/bin/mutalyzer-batchd
index c7bd01759acf86c1e03d674ef74765cc215361b8..d02c323829b033d3a72844b80a16e18ce3f13699 100755
--- a/bin/mutalyzer-batchd
+++ b/bin/mutalyzer-batchd
@@ -8,6 +8,7 @@ should be run with the mutalyzer directory as working directory.
 
 @todo: Check if PID dir is writable.
 @todo: Get rid of ugly exception logging.
+@todo: Reload configuration without restarting (for example, on SIGHUP).
 
 [1] http://pypi.python.org/pypi/python-daemon/
 """
diff --git a/extras/apache/mutalyzer.conf b/extras/apache/mutalyzer.conf
new file mode 100644
index 0000000000000000000000000000000000000000..fdd3382000e1c90057bc3b81cf6ff6e7ef4a15f0
--- /dev/null
+++ b/extras/apache/mutalyzer.conf
@@ -0,0 +1,10 @@
+Alias /mutalyzer/base <MUTALYZER_PACKAGE_ROOT>/templates/base
+
+WSGIScriptAlias /mutalyzer/services <MUTALYZER_PACKAGE_ROOT>/webservice.py
+WSGIScriptAlias /mutalyzer <MUTALYZER_PACKAGE_ROOT>/wsgi.py
+
+<Directory <MUTALYZER_PACKAGE_ROOT>/>
+    Order deny,allow
+    Allow from all
+    AllowOverride None
+</Directory>
diff --git a/extras/init.d/mutalyzer-batchd b/extras/init.d/mutalyzer-batchd
old mode 100755
new mode 100644
index 9c559f2427f89b7c2dadff17468eaaf6c3002b28..c94763440847e1172d77c14247a0ea694dd85817
--- a/extras/init.d/mutalyzer-batchd
+++ b/extras/init.d/mutalyzer-batchd
@@ -1,6 +1,6 @@
 #! /bin/sh
 ### BEGIN INIT INFO
-# Provides:          mutalyzer-batch-daemon
+# Provides:          mutalyzer-batchd
 # Required-Start:    $local_fs $remote_fs $network $syslog $mysql
 # Required-Stop:     $local_fs $remote_fs $network $syslog $mysql
 # Default-Start:     2 3 4 5
@@ -9,26 +9,21 @@
 # Description:       Controls the Mutalyzer batch job processing daemon..
 ### END INIT INFO
 
-# Author: Martijn Vermaat <m.vermaat.hg@lumc.nl>
-
-# Do NOT "set -e"
-
-# PATH should only include /usr/* if it runs after the mountnfs.sh script
 PATH=/sbin:/usr/sbin:/bin:/usr/bin
 DESC="Mutalyzer batch deamon"
-DAEMON=/home/martijn/projects/mutalyzer/svn/branches/refactor-mutalyzer-branch/bin/mutalyzer-batchd
-DIR=/home/martijn/projects/mutalyzer/svn/branches/refactor-mutalyzer-branch
 NAME=mutalyzer-batchd
-PIDFILE=/var/run/mutalyzer/mutalyzer-batchd.pid
+DAEMON=<MUTALYZER_BIN_BATCHD>
+DIR=<MUTALYZER_PACKAGE_ROOT>
 PIDDIR=/var/run/mutalyzer
-SCRIPTNAME=/etc/init.d/mutalyzer-batchd
+PIDFILE=$PIDDIR/$NAME.pid
+SCRIPTNAME=/etc/init.d/$NAME
 USER=www-data
 
 # Exit if the package is not installed
 [ -x "$DAEMON" ] || exit 0
 
 # Read configuration variable file if it is present
-[ -r /etc/default/mutalyzer ] && . /etc/default/mutalyzer
+[ -r /etc/default/$NAME ] && . /etc/default/$NAME
 
 # Load the VERBOSE setting and other rcS variables
 . /lib/init/vars.sh
diff --git a/extras/post-install.sh b/extras/post-install.sh
index 35ff4468f0f4cd0356409dd132d46e74845d8fdb..1f96e26eaf923f73150645adc9d71d08960b0533 100644
--- a/extras/post-install.sh
+++ b/extras/post-install.sh
@@ -8,9 +8,17 @@
 
 # Todo:
 # - Database setup
+# - Apache setup
 # - Copy doc to /usr/share/doc
 
-if [ ! -f /etc/mutalyzer/config ]; do
+set -e
+
+# The 'cd /' is a hack to prevent the mutalyzer package under the current
+# directory to be used.
+PACKAGE_ROOT=$(cd / && python -c 'import mutalyzer; print mutalyzer.package_root()')
+BIN_BATCHD=$(which mutalyzer-batchd)
+
+if [ ! -e /etc/mutalyzer/config ]; then
     mkdir -p /etc/mutalyzer
     cp extras/config.example /etc/mutalyzer/config
     chmod -R u=rwX,go=rX /etc/mutalyzer
@@ -24,7 +32,14 @@ mkdir -p /var/cache/mutalyzer
 chown -R www-data:www-data /var/cache/mutalyzer
 chmod -R u=rwX,go=rX /var/cache/mutalyzer
 
-if [ ! -f /etc/init.d/mutalyzer-batchd ]; do
+if [ ! -e /etc/init.d/mutalyzer-batchd ]; then
     cp extras/init.d/mutalyzer-batchd /etc/init.d/mutalyzer-batchd
+    sed -i -e "s@<MUTALYZER_PACKAGE_ROOT>@${PACKAGE_ROOT}@g" -e "s@<MUTALYZER_BIN_BATCHD>@${BIN_BATCHD}@g" /etc/init.d/mutalyzer-batchd
     chmod u=rwx,go=rx /etc/init.d/mutalyzer-batchd
 fi
+
+if [ ! -e /etc/apache2/conf.d/mutalyzer.conf ]; then
+    cp extras/apache/mutalyzer.conf /etc/apache2/conf.d/mutalyzer.conf
+    sed -i -e "s@<MUTALYZER_PACKAGE_ROOT>@${PACKAGE_ROOT}@g" -e "s@<MUTALYZER_BIN_BATCHD>@${BIN_BATCHD}@g" /etc/apache2/conf.d/mutalyzer.conf
+    chmod u=rw,go=r /etc/apache2/conf.d/mutalyzer.conf
+fi
diff --git a/mutalyzer/__init__.py b/mutalyzer/__init__.py
index 693f197560ee2f2d32fddf0d7fb371be0138e2d9..20be9eafb9d58e0c583d4b3edfb88acc09a260be 100644
--- a/mutalyzer/__init__.py
+++ b/mutalyzer/__init__.py
@@ -1,6 +1,9 @@
 """HGVS variant nomenclature checker."""
 
 
+import os
+
+
 # On the event of a new release, we update the __version_info__ and __date__
 # package globals and set RELEASE to True.
 # After a release, a development version is denoted by a __version_info__
@@ -21,3 +24,7 @@ __homepage__ = 'http://mutalyzer.nl'
 
 NOMENCLATURE_VERSION_INFO = ('2', '0')
 NOMENCLATURE_VERSION = '.'.join(NOMENCLATURE_VERSION_INFO)
+
+
+def package_root():
+    return os.path.split(__file__)[0]
diff --git a/mutalyzer/wsgi.py b/mutalyzer/wsgi.py
index 311dd6e76d36d2cf7a1f26ab7eca2ce05c0909e1..4bd4f47e9ded55c84db8412644b276163599a29e 100644
--- a/mutalyzer/wsgi.py
+++ b/mutalyzer/wsgi.py
@@ -85,6 +85,7 @@ config = Config()
 
 # URL dispatch table
 urls = (
+    '',                     'RedirectHome',
     '/(index)?',            'Static',
     '/(about)',             'Static',
     '/(help)',              'Static',
@@ -204,6 +205,23 @@ render = render_tal('templates', globals={
 app = web.application(urls, globals(), autoreload=False)
 
 
+class RedirectHome:
+    """
+    Permanent redirect to the homepage.
+    """
+    def GET(self):
+        """
+        Redirect to / and include the query string.
+        """
+        raise web.redirect('/' + web.ctx.query)
+
+    def POST(self):
+        """
+        Redirect to / and include the query string.
+        """
+        raise web.redirect('/' + web.ctx.query)
+
+
 class Download:
     """
     Download file from template directory, formatting it first.
@@ -1107,5 +1125,6 @@ if __name__ == '__main__':
 else:
     # WSGI application
     # Todo: Fix Mutalyzer to not depend on working directory
-    os.chdir(os.path.dirname(__file__))
+    #os.chdir(os.path.dirname(__file__))
+    os.chdir(mutalyzer.package_root())
     application = app.wsgifunc()
diff --git a/setup.py b/setup.py
index 64219d5b7403d7fa009e76ee04beb600ee506286..33e002f72b06b7d73e4818c6758af4ea37cc0870 100644
--- a/setup.py
+++ b/setup.py
@@ -27,4 +27,4 @@ setup(
 # - Chown /var/log/mutalyzer.log and /var/cache/mutalyzer
 # - Copy extras/init.d/mutalyzer-batchd to /etc/init.d/mutalyzer-batchd
 # - Copy doc to /usr/share/doc
-# Perhaps as a postinstall script?
+# Check extras/post-install.sh for these.
diff --git a/tests/config b/tests/config
new file mode 100644
index 0000000000000000000000000000000000000000..4fb75eab7966b6f9fbc576da69f2211a7df88de3
--- /dev/null
+++ b/tests/config
@@ -0,0 +1,157 @@
+#
+# Mutalyzer config file.
+#
+# Copy this file to /etc/mutalyzer/config or ~/.config/mutalyzer/config and
+# modify to suit your preferences.
+
+#
+# These settings are used by the Retriever module.
+#
+
+# Use this email address for retrieval of records at the NCBI.
+email = "m.vermaat.hg@lumc.nl"
+
+# The cache directory.
+cache = "/var/cache/mutalyzer"
+
+# The maximum size of the cache in megabytes.
+cachesize = 50
+
+# The maximum size of a downloaded GenBank file in megabytes.
+maxDldSize = 10
+
+# The minimum size of a downloaded GenBank file in bytes.
+minDldSize = 512
+
+# The URL from where LRG files are fetched
+lrgurl = "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/"
+
+
+#
+# These settings are used by the Db module.
+#
+
+# Internal database.
+internalDb = "mutalyzer"
+
+# MySQL mapping database names.
+dbNames = "hg18", "hg19"
+
+# MySQL username for the local databases (internalDb and dbNames).
+LocalMySQLuser = "mutalyzer"
+
+# Host name for the local databases.
+LocalMySQLhost = "localhost"
+
+# MySQL username for the UCSC database.
+RemoteMySQLuser = "genome"
+
+# Host name for the UCSC database.
+RemoteMySQLhost = "genome-mysql.cse.ucsc.edu"
+
+# Retrieve all entries modified within a certain number of days.
+UpdateInterval = 7
+
+
+#
+# These settings are used by the Output module.
+#
+
+# Name and location of the log file.
+log = "/tmp/mutalyzer-tests.log"
+
+# Prefix for each log message.
+datestring = "%Y-%m-%d %H:%M:%S"
+
+# Message levels:
+#
+# 0 : Debug   ; Show all messages.
+# 1 : Info    ; Show all messages except debug messages.
+# 2 : Warning ; Show warning, error and fatal messages.
+# 3 : Error   ; Show error and fatal messages.
+# 4 : Fatal   ; Only show fatal messages.
+# 5 : Off     ; Show nothing.
+
+# Level of logged messages.
+loglevel = 3
+
+# Level of output messages.
+outputlevel = 1
+
+
+#
+# These settings are used by the Mutator module.
+#
+
+# Length of the flanking sequences (used in the visualisation of mutations).
+flanksize = 25
+
+# Maximum length of visualised mutations.
+maxvissize = 25
+
+# Length of the flanking sequences of the clipped mutations (see maxvissize).
+flankclipsize = 6
+
+
+#
+# These settings are used by the Scheduler module.
+#
+
+# Name of the batch process.
+processName = "MutalyzerBatch2"
+
+# Return e-mail address.
+mailFrom = "noreply@humgen.nl"
+
+# Subject of the message.
+mailSubject = "Result of Mutalyzer batch check."
+
+# Location of the results.
+resultsDir = "/var/cache/mutalyzer"
+
+# Location of the PID file.
+PIDfile = "/var/run/mutalyzer/mutalyzer-batchd.pid"
+
+# Maximum size for uploaded batch input files in megabytes.
+batchInputMaxSize = 5
+
+# The output header for NameChecking
+nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins"
+
+# The output header for SyntaxChecking
+syntaxCheckOutHeader = "Input", "Status"
+
+# The output header for PositionConverter
+positionConverterOutHeader = "Input Variant", "Errors", "Chromosomal Variant", "Coding Variant(s)"
+
+# The output header for SnpConverter
+snpConverterOutHeader = "Input Variant", "HGVS description(s)", "Errors | Messages"
+
+
+#
+# These settings are used by the File module.
+#
+
+# Amount of bytes to be read for determining the file type.
+bufSize = 32768
+
+# The obligatory header in batch request files.
+header = "AccNo", "Genesymbol", "Mutation"
+
+# Threshold for Batch Jobs
+threshold = 0.05
+
+
+#
+# These settings are used by the GenRecord module.
+#
+
+# Number of upstream nucleotides when searching for a transcript.
+upstream = 5000
+
+# Number of downstream nucleotides when searching for a transcript.
+downstream = 2000
+
+spliceAlarm = 2
+
+spliceWarn = 5
diff --git a/tests/test_grammar.py b/tests/test_grammar.py
index 85ab8276a695d6904938742c3066e8a47408026c..c5564a80ccfa152ff6c559b5d4be68de1aeaef46 100644
--- a/tests/test_grammar.py
+++ b/tests/test_grammar.py
@@ -7,14 +7,17 @@ Tests for the mutalyzer.grammar module.
 import os
 from nose.tools import *
 
+import mutalyzer
 from mutalyzer.config import Config
 from mutalyzer.grammar import Grammar
 from mutalyzer.output import Output
 
 
+# If we remove the os.chdir below, this is no longer necessary
+CONFIG = os.path.realpath('config')
+
 # Todo: Fix Mutalyzer to not depend on working directory
-root_dir = os.path.split(os.path.dirname(__file__))[0]
-os.chdir(os.path.join(root_dir, 'mutalyzer'))
+os.chdir(mutalyzer.package_root())
 
 
 class TestGrammar():
@@ -26,7 +29,7 @@ class TestGrammar():
         """
         Initialize test Grammar instance.
         """
-        self.config = Config()
+        self.config = Config(CONFIG)
         self.output = Output(__file__, self.config.Output)
         self.grammar = Grammar(self.output)
 
diff --git a/tests/test_mutalyzer.py b/tests/test_mutalyzer.py
index 5304bb170237a467b4cc24af7b9f4d6877d0037d..52ecf1240f533fd5057ece8e57de26cd106577f0 100644
--- a/tests/test_mutalyzer.py
+++ b/tests/test_mutalyzer.py
@@ -10,14 +10,17 @@ import random
 from nose.tools import *
 from Bio.Seq import Seq
 
+import mutalyzer
 from mutalyzer.config import Config
 from mutalyzer.output import Output
 from mutalyzer.variantchecker import check_variant
 
 
+# If we remove the os.chdir below, this is no longer necessary
+CONFIG = os.path.realpath('config')
+
 # Todo: Fix Mutalyzer to not depend on working directory
-root_dir = os.path.split(os.path.dirname(__file__))[0]
-os.chdir(os.path.join(root_dir, 'mutalyzer'))
+os.chdir(mutalyzer.package_root())
 
 
 class TestMutalyzer():
@@ -29,7 +32,7 @@ class TestMutalyzer():
         """
         Initialize test Mutalyzer module.
         """
-        self.config = Config()
+        self.config = Config(CONFIG)
         self.output = Output(__file__, self.config.Output)
 
     def test_roll(self):
diff --git a/tests/test_mutator.py b/tests/test_mutator.py
index 766270d44703de14984d2877cf056cf935b17e58..b0bf933f5098597d4760a5af8ede0b493715a926 100644
--- a/tests/test_mutator.py
+++ b/tests/test_mutator.py
@@ -10,14 +10,17 @@ import random
 from nose.tools import *
 from Bio.Seq import Seq
 
+import mutalyzer
 from mutalyzer.config import Config
 from mutalyzer.output import Output
 from mutalyzer import mutator
 
 
+# If we remove the os.chdir below, this is no longer necessary
+CONFIG = os.path.realpath('config')
+
 # Todo: Fix Mutalyzer to not depend on working directory
-root_dir = os.path.split(os.path.dirname(__file__))[0]
-os.chdir(os.path.join(root_dir, 'mutalyzer'))
+os.chdir(mutalyzer.package_root())
 
 
 def _seq(length):
@@ -39,7 +42,7 @@ class TestMutator():
         """
         Initialize test mutator module.
         """
-        self.config = Config()
+        self.config = Config(CONFIG)
         self.output = Output(__file__, self.config.Output)
 
     def _mutator(self, sequence):
@@ -178,7 +181,7 @@ class TestMutator():
         sites = [4, 9, 14, 17, 25, 27]
         m = self._mutator(_seq(l))
         m.delM(17, 17)   # g.17del
-        assert_equal(m.newSplice(sites), [4, 9, 14, 16, 24, 27])
+        assert_equal(m.newSplice(sites), [4, 9, 14, 16, 24, 26])
 
     def test_newSplice_don_del_after(self):
         """
diff --git a/tests/test_webservice.py b/tests/test_webservice.py
index 2b264f21900651a9c1eb5c3de2b2869be380f16d..df94d12376001a46248f3daed17560b074a13277 100644
--- a/tests/test_webservice.py
+++ b/tests/test_webservice.py
@@ -10,7 +10,7 @@ from suds import WebFault
 from nose.tools import *
 
 
-WSDL_URL = 'http://mutalyzer-refactor.martijn/services/?wsdl'
+WSDL_URL = 'http://localhost/mutalyzer/services/?wsdl'
 
 
 class TestWSDL():
diff --git a/tests/test_wsgi.py b/tests/test_wsgi.py
index fc8d49643d21f89feec6783ab5030c28c703f46d..f5e399207bd4d792f44eb91c7a2835e7b65e57e1 100644
--- a/tests/test_wsgi.py
+++ b/tests/test_wsgi.py
@@ -18,12 +18,12 @@ import time
 from nose.tools import *
 from webtest import TestApp
 
+import mutalyzer
 from mutalyzer.wsgi import application
 
 
 # Todo: Fix Mutalyzer to not depend on working directory
-root_dir = os.path.split(os.path.dirname(__file__))[0]
-os.chdir(os.path.join(root_dir, 'mutalyzer'))
+os.chdir(mutalyzer.package_root())
 
 
 class TestWSGI():