# HG changeset patch
# User bgruening
# Date 1369258320 14400
# Node ID f3f7868cdfaccbd1be5fe6d3e28ba094af875e3a
# Parent  dfa05117e30ac754f60a05e3c2fed3aeec05e355
Uploaded

diff -r dfa05117e30a -r f3f7868cdfac repository_dependencies.xml
--- a/repository_dependencies.xml	Tue May 14 17:03:28 2013 -0400
+++ b/repository_dependencies.xml	Wed May 22 17:32:00 2013 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="1b63345907ec" />
-</repositories> 
+    <repository changeset_revision="1b63345907ec" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>
\ No newline at end of file
diff -r dfa05117e30a -r f3f7868cdfac tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 14 17:03:28 2013 -0400
+++ b/tool_dependencies.xml	Wed May 22 17:32:00 2013 -0400
@@ -1,73 +1,70 @@
+<?xml version="1.0"?>
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="dc6a907dd737" prior_installation_required="True" />
+        <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="graphicsmagick" version="1.3.18">
+        <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="osra" version="1.4.0">
         <install version="1.0">
             <actions>
-                <!-- first action is always downloading -->
+                
                 <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz</action>
 
-                <!-- populate the environment variables from the dependend repos -->
+                
                 <action type="set_environment_for_install">
-                    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="dc6a907dd737">
+                    <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="openbabel" version="2.3.2" />
                     </repository>
+                    <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="graphicsmagick" version="1.3.18" />
+                    </repository>
                 </action>
 
-                <!--compiling GraphicsMagick-1.3.18 -->
-                <action type="shell_command">wget http://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.18/GraphicsMagick-1.3.18.tar.gz</action>
-                <action type="shell_command">tar xfvz GraphicsMagick-1.3.18.tar.gz &amp;&amp; cd GraphicsMagick-1.3.18 &amp;&amp; ./configure --prefix=$INSTALL_DIR/gmagick/build --enable-shared=yes &amp;&amp; make &amp;&amp; make install</action>
-
-                <!--compiling potrace-1.11 -->
+                
                 <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action>
                 <action type="shell_command">tar xfvz potrace-1.11.tar.gz &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
 
-                <!--compiling gocr 0.50patched -->
+                
                 <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
                 <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
 
-                <!--compiling tclap 1.2.1 -->
+                
                 <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action>
                 <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
 
-
-                <!--compiling ocrad 0.21 -->
+                
                 <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
                 <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
 
-                <!--compiling openbabel 2.3.2 
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz</action>
-                <action type="shell_command">tar xfvz openbabel-2.3.2.tar.gz &amp;&amp; cd openbabel-2.3.2 &amp;&amp; cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/openbabel/build &amp;&amp; make &amp;&amp; make install</action>
-                -->
-                <!--compiling cuneiform 1.1.0 -->
+                
                 <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action>
                 <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
 
-                <!--And finally OSRA 1.4.0-->
-                <!--<action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz</action>-->
+                
                 <action type="shell_command">wget http://share.gruenings.eu/osra-1.4.0-configure.patch</action>
                 <action type="shell_command">patch configure &lt; osra-1.4.0-configure.patch</action>
-                <!-- Extending the PATH is needed for OSRA -->
-                <action type="shell_command">export PATH=$PATH:$INSTALL_DIR/gmagick/build/bin/ &amp;&amp; ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$INSTALL_DIR/gmagick/build/lib/ --with-graphicsmagick-include=$INSTALL_DIR/gmagick/build/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
+                
+                <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/gmagick/bin/ &amp;&amp; ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/gmagick/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/gmagick/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install</action>
 
                 <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action>
-                <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>-->
+                
                 <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action>
                 <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action>
                 <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action>
 
                 <action type="set_environment">
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/gmagick/build/lib/</environment_variable>
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/potrace/build/lib/</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA -->
-                    <environment_variable name="OSRA_DATA_FILES" action="set_to">$INSTALL_DIR/share</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$GRAPHICSMAGICK_ROOT_DIR/gmagick/lib/</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    
+                    <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable>
                 </action>
             </actions>
         </install>
         <readme>We still have a handfull of requirements</readme>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file