diff --git a/EMBOSS.spec b/EMBOSS.spec
index 0a5dee2..e23d3a0 100644
--- a/EMBOSS.spec
+++ b/EMBOSS.spec
@@ -5,7 +5,7 @@
 
 Name:           EMBOSS
 Version:        6.1.0
-Release:        5%{?dist}
+Release:        6%{?dist}
 Summary:        The European Molecular Biology Open Software Suite
 
 Group:          Applications/Engineering
@@ -13,22 +13,28 @@ License:        GPLv2+
 URL:            http://emboss.sf.net/
 Source0:        ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
 Source1:        README.fixes
+Source2:        jemboss.desktop
 #Upstream patch
-Patch0:         ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz
+Patch0:         ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz
 #Use system-wide pcre. Sent upstream.
 Patch1:         %{name}-system-pcre.patch
 #Fedora-specific. Not sent upstream.
 Patch2:         %{name}-fedora.patch
-#Add missing destdir. Sent upstream.
+#Remove extra destdir. Sent upstream.
 Patch3:         %{name}-6.1.0-destdir.patch
+#Patch ensuring jemboss rebuild backported from CVS
+Patch4:         %{name}-6.1.0-rebuild.patch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
+BuildRequires:  ant
+BuildRequires:  desktop-file-utils
 BuildRequires:  gd-devel
-#BuildRequires:  java-devel
+BuildRequires:  java-devel >= 1:1.6.0
+BuildRequires:  jpackage-utils
 BuildRequires:  pam-devel
 BuildRequires:  pcre-devel
-#BuildRequires:  axis classpathx-jaf jakarta-commons-discovery
-#BuildRequires:  jakarta-commons-logging log4j wsdl4j
+BuildRequires:  axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
+BuildRequires:  log4j regexp servlet xerces-j2 wsdl4j
 
 %description
 EMBOSS is a new, free Open Source software analysis package specially
@@ -64,14 +70,16 @@ The %{name}-libs package includes the dynamic libraries
 necessary for %{name}.
 
 
-#%package java
+#%package -n jemboss
 #Summary:        Java interface to %{name}
 #Group:          Applications/Engineering
 #Requires:       %{name} = %{version}-%{release}
-#Requires:       axis classpathx-jaf jakarta-commons-discovery
-#Requires:       jakarta-commons-logging log4j wsdl4j
+#Requires:       java >= 1:1.6.0
+#Requires:       jpackage-utils    
+#Requires:       axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
+#Requires:       log4j regexp servlet xerces-j2 wsdl4j
 
-#%description java
+#%description -n jemboss
 #Jemboss is a Java interface to EMBOSS, developed at
 #the HGMP-RC and in close collaboration with the EMBOSS
 #development team. It is distributed as part of the EMBOSS
@@ -87,6 +95,7 @@ necessary for %{name}.
 %patch1 -p1 -b .pcre
 %patch2 -p0 -b .fedora
 %patch3 -p0 -b .destdir
+%patch4 -p0 -b .jemboss-rebuild
 
 #install the patch readme
 install -pm 644 %{SOURCE1} README.fixes
@@ -94,30 +103,29 @@ install -pm 644 %{SOURCE1} README.fixes
 #these files were executable for some reason
 chmod 644 emboss/prettyplot.c emboss/polydot.c emboss/supermatcher.c
 
+#use newer log4j version
+sed -i "s@log4j-1.2.8@log4j-1.2.14@" \
+    jemboss/lib/axis/Makefile.am \
+    jemboss/lib/axis/Makefile.in \
+    jemboss/utils/makeFileManagerJNLP.sh \
+    jemboss/utils/makeJNLP.sh
+
 #use system java libraries
-#pushd jemboss/lib
-#rm activation.jar;
-#ln -s %{_javadir}/activation.jar activation.jar;
-#pushd axis
-#for i in axis-ant axis jaxrpc saaj;
-#do
-#    rm $i.jar;
-#    ln -s %{_javadir}/axis/$i.jar $i.jar;
-#done
-#for i in commons-discovery commons-logging wsdl4j;
-#do
-#    rm $i.jar;
-#    ln -s %{_javadir}/$i.jar $i.jar;
-#done
-#rm log4j-1.2.8.jar
-#ln -s %{_javadir}/log4j.jar log4j-1.2.8.jar
-#popd
-#popd
+rm jemboss/lib/{activation,client,jakarta-regexp-1.2,mail,xerces}.jar
+build-jar-repository -s -p jemboss/lib activation regexp javamail xerces-j2
+mv jemboss/lib/regexp.jar jemboss/lib/jakarta-regexp-1.2.jar
+mv jemboss/lib/javamail.jar jemboss/lib/mail.jar
+mv jemboss/lib/xerces-j2.jar jemboss/lib/xerces.jar
+rm jemboss/lib/axis/*.jar
+build-jar-repository -s -p jemboss/lib/axis axis/axis-ant axis/axis axis/jaxrpc axis/saaj commons-discovery commons-logging log4j-1.2.14 servlet wsdl4j
+for i in axis axis-ant jaxrpc saaj;
+do
+mv jemboss/lib/axis/axis_$i.jar jemboss/lib/axis/$i.jar;
+done
 
 
 %build
 %configure \
-  --without-java \
   --disable-static \
   --with-x \
   --with-auth \
@@ -126,6 +134,9 @@ chmod 644 emboss/prettyplot.c emboss/polydot.c emboss/supermatcher.c
 %ifarch ppc64 sparc64 x86_64
   --enable-64 \
 %endif
+  --with-java=/usr/lib/jvm/java/include \
+  --with-javaos=/usr/lib/jvm/java/include/linux \
+
 
 %{__make} %{?_smp_mflags}
 
@@ -169,6 +180,11 @@ popd
 #rename conflicting binaries
 mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos
 
+#install the desktop file
+#desktop-file-install                                    \
+#--dir=${RPM_BUILD_ROOT}%{_datadir}/applications         \
+#%{SOURCE2}
+
 
 %clean
 rm -rf $RPM_BUILD_ROOT
@@ -196,20 +212,34 @@ rm -rf $RPM_BUILD_ROOT
 %{_libdir}/*.so
 %{_includedir}/EMBOSS
 
+
 %files libs
 %defattr(-,root,root,-)
 %{_libdir}/*.so.*
 
 
-#%files java
+#%files -n jemboss
 #%defattr(-,root,root,-)
 #%doc jemboss/README jemboss/resources jemboss/api
 #%{_bindir}/runJemboss.csh
 #%{_bindir}/jembossctl
+#%{_datadir}/applications/jemboss.desktop
 #%{_datadir}/EMBOSS/jemboss
 
 
 %changelog
+* Sun Dec 13 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-6
+- Added the upstream 1-3 patch
+- Fixed bogus Patch3 description
+- Jemboss is still disabled, but some improvements have been made
+  - Backported patch enabling jemboss rebuild from CVS
+  - Added ant and jpackage-utils to BuildRequires
+  - Made java-devel dependency versioned
+  - Switched to build-jar-repository to fill the dependencies
+  - Replaced versioned log4j calls with latest version
+  - Renamed EMBOSS-java to jemboss
+  - Added a desktop entry for jemboss from Debian
+
 * Sat Oct 17 2009 Julian Sikorski <belegdol@fedoraproject.org> - 6.1.0-5
 - Added comments explaining the purpose of each patch