--- a/tool_dependencies.xml	Thu Apr 16 10:37:28 2015 -0400
+++ b/tool_dependencies.xml	Mon Apr 20 11:09:24 2015 -0400
@@ -1,83 +1,40 @@
 <?xml version="1.0"?>
-<!-- ToDo can we get it easily without svn? Is this included in the final tarball? -->
-<!-- svn checkout http://svn.code.sf.net/p/open-ms/code/THIRDPARTY/SEARCHENGINES/Linux/64bit/ _searchengines -->
 <tool_dependency>
-    <package name="openms" version="2.0">
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="psort" version="3.0.3">
         <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/openms/openms-2.0-Linux-x86_64.tar.gz</action>
-                    <action type="shell_command">rm openms-2.0-Linux-x86_64.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                    <action type="set_environment">
-                        <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                        <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
-                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
-                    </action>
-                </actions>
-                <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">https://github.com/OpenMS/OpenMS/archive/develop.tar.gz</action>
-                    <action type="download_by_url">https://github.com/OpenMS/contrib/archive/master.tar.gz</action>
-                    <action type="shell_command">mv contrib-master ../contrib</action>
-                    <package name="libtool" version="2.4">
-                        <repository name="package_libtool_2_4" owner="iuc" prior_installation_required="True" />
-                    </package>
-                    <package name="Qt" version="4.8">
-                        <repository name="package_qt_4_8" owner="iuc" prior_installation_required="True" />
-                    </package>
-                    <package name="zlib" version="1.2.8">
-                        <repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" />
-                    </package>
-                    <package name="bzlib" version="1.0.6">
-                        <repository name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" />
-                    </package>
-                    <action type="set_environment_for_install">
-                        <repository name="package_libtool_2_4" owner="iuc">
-                            <package name="libtool" version="2.4" />
-                        </repository>
-                        <repository name="package_qt_4_8" owner="iuc">
-                            <package name="Qt" version="4.8" />
-                        </repository>
-                        <repository name="package_zlib_1_2_8" owner="iuc">
-                            <package name="zlib" version="1.2.8" />
-                        </repository>
-                        <repository name="package_bzlib_1_0" owner="iuc">
-                            <package name="bzlib" version="1.0.6" />
-                        </repository>
-                    </action>
-                    <action type="change_directory">../contrib</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=SEQAN</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=LIBSVM</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=XERCESC</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=GSL</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=BOOST -DNUMBER_OF_JOBS=4</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=COINOR</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=BZIP2</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=GLPK</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=EIGEN</action>
-                    <action type="shell_command">cmake . -DBUILD_TYPE=WILDMAGIC</action>
+            <actions>
+                <action type="download_by_url">http://www.psort.org/download/libpsortb-1.0.tar.gz</action>
+                <action type="autoconf" />
+
+                <action type="download_by_url">ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/pft2.3.5.d.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/pft</destination_directory>
+                </action>
 
-                    <action type="change_directory">..</action>
-                    <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF</action>
-                    <action type="shell_command">make OpenMS TOPP UTILS</action>
-                    <action type="shell_command">make install</action>
-                    <action type="set_environment">
-                        <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                        <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
-                        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
-                        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[QT_ROOT_DIR]/lib/</environment_variable>
-                    </action>
-                </actions>
-            </actions_group>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="LIBPSORTB_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/pft</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
+                </action>
+
+                <action type="setup_perl_environment">
+                    <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                   <!-- allow downloading and installing an Perl package from cpan.org-->
+                   <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
+                   <package>http://www.psort.org/download/bio-tools-psort-all.3.0.3.tar.gz</package>
+                </action>
+            </actions>
         </install>
         <readme>
-            This package downloads and installs OpenMS.
-            http://open-ms.sourceforge.net/
+            http://www.psort.org/downloads/index.html
         </readme>
     </package>
 </tool_dependency>