# HG changeset patch
# User bgruening
# Date 1366902309 14400
# Node ID 3b50c1d0d1e53c7443e31995e53c972355aa5d64
# Parent  deccc074dbfb0b5a7006ef8edc75033a11c5d792
Uploaded

diff -r deccc074dbfb -r 3b50c1d0d1e5 osra.py
--- a/osra.py	Fri Apr 12 18:14:31 2013 -0400
+++ b/osra.py	Thu Apr 25 11:05:09 2013 -0400
@@ -5,7 +5,8 @@
 
 """
     OSRA_DATA_FILES is set during the toolshed Installation
-    if it is not set, use the standard configuration of OSRA and hope the best.
+    If it is not set, use the standard configuration of OSRA. 
+    That means we need to delete argument 4-7.
     That script is a hack, because we do not know the content of OSRA_DATA_FILES at xml evaluation time.
 
     osra -f $oformat $infile 
diff -r deccc074dbfb -r 3b50c1d0d1e5 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 12 18:14:31 2013 -0400
+++ b/tool_dependencies.xml	Thu Apr 25 11:05:09 2013 -0400
@@ -1,8 +1,20 @@
 <tool_dependency>
+    <package name="openbabel" version="2.3.2">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="6fd6b904eeff" prior_installation_required="True" />
+    </package>
     <package name="osra" version="1.4.0">
         <install version="1.0">
             <actions>
+                <!-- first action is always downloading -->
                 <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz</action>
+
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="6fd6b904eeff">
+                        <package name="openbabel" version="2.3.2" />
+                    </repository>
+                </action>
+
                 <!--compiling GraphicsMagick-1.3.18 -->
                 <action type="shell_command">wget http://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.18/GraphicsMagick-1.3.18.tar.gz</action>
                 <action type="shell_command">tar xfvz GraphicsMagick-1.3.18.tar.gz &amp;&amp; cd GraphicsMagick-1.3.18 &amp;&amp; ./configure --prefix=$INSTALL_DIR/gmagick/build --enable-shared=yes &amp;&amp; make &amp;&amp; make install</action>
@@ -24,10 +36,10 @@
                 <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 -->
+                <!--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>
@@ -37,12 +49,12 @@
                 <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=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ --with-openbabel-lib=$INSTALL_DIR/openbabel/build/lib/ --with-graphicsmagick-lib=$INSTALL_DIR/gmagick/build/lib/ --with-graphicsmagick-include=$INSTALL_DIR/gmagick/build/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
+                <action type="shell_command">export PATH=$PATH:$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">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/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>