--- a/tool_dependencies.xml	Mon Oct 14 04:36:52 2013 -0400
+++ b/tool_dependencies.xml	Tue Oct 15 04:19:33 2013 -0400
@@ -13,7 +13,6 @@
         <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
-
     <package name="helperlibs" version="0.1.2">
         <install version="1.0">
             <actions>
@@ -84,7 +83,8 @@
     <package name="antismash" version="2.0.2">
         <install version="1.0">
            <actions_group>
-                <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
+
+                <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. -->
                 <actions architecture="x86_64" os="darwin">
                     <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
                     <action type="move_directory_files">
@@ -94,6 +94,43 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
+                        we need to copy this plugin into the correct location.
+                    -->
+                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
+                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
+                    <action type="move_file">
+                        <source>__init__.py</source>
+                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
+                    </action>
+                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
+                        do not offer the option for genprediction and do not install glimmer and Co.
+                        For that reason deactivate the check.
+                    -->
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
+                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
+                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>n&gt;
+                </actions>
+
+                <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. -->
+                <actions architecture="i386" os="darwin">
+                    <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                    <action type="chmod">
+                        <file mode="750">$INSTALL_DIR/run_antismash.py</file>
+                    </action>
+                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
+                        we need to copy this plugin into the correct location.
+                    -->
+                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
+                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
+                    <action type="move_file">
+                        <source>__init__.py</source>
+                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
+                    </action>
                     <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
@@ -102,24 +139,7 @@
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
-                <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
-                <actions architecture="i386" os="darwin">
-                    <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                    <action type="chmod">
-                        <file mode="750">$INSTALL_DIR/run_antismash.py</file>
-                    </action>
-                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
-                        do not offer the option for genprediction and do not install glimmer and Co.
-                        For that reason deactivate the check.
-                    -->
-                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
-                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
-                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
-                </actions>
+
                 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
                 <actions architecture="x86_64" os="linux">
                     <action target_filename="antismash-2.0.2.tar.bz2" type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action>
@@ -147,6 +167,7 @@
                     <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
+
                 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
                 <actions architecture="i386" os="linux">
                     <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action>
@@ -157,6 +178,15 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <!-- As last step we created an additional output plugin, that generates protein FASTA files from all clusters and
+                        we need to copy this plugin into the correct location.
+                    -->
+                    <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>
+                    <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>
+                    <action type="move_file">
+                        <source>__init__.py</source>
+                        <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>
+                    </action>
                     <!-- AntiSmash has a prerequirement check that is not useful for us, because we
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.