# HG changeset patch
# User bgruening
# Date 1369344605 14400
# Node ID f265bcf0ddc5f354306c8ae6d8ea4644bdae13ee
# Parent  143a63ca2bca45ae50351041109c0e857628348f
Uploaded

diff -r 143a63ca2bca -r f265bcf0ddc5 repository_dependencies.xml
--- a/repository_dependencies.xml	Thu May 23 16:19:16 2013 -0400
+++ b/repository_dependencies.xml	Thu May 23 17:30:05 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 changeset_revision="1b63345907ec" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="bd886859b184" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 143a63ca2bca -r f265bcf0ddc5 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 23 16:19:16 2013 -0400
+++ b/tool_dependencies.xml	Thu May 23 17:30:05 2013 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-        <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ccda1b8ebc72" 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" />
@@ -14,7 +14,7 @@
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="ccda1b8ebc72" 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">
diff -r 143a63ca2bca -r f265bcf0ddc5 tool_dependencies_1_4.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies_1_4.xml	Thu May 23 17:30:05 2013 -0400
@@ -0,0 +1,69 @@
+<tool_dependency>
+    <package name="openbabel" version="2.3.2">
+        <repository name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" />
+    </package>
+    <package name="graphicsmagick" version="1.3.18">
+        <repository name="package_graphicsmagick_1_3" owner="bgruening" 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 name="package_openbabel_2_3" owner="bgruening">
+                        <package name="openbabel" version="2.3.2" />
+                    </repository>
+                    <repository name="package_graphicsmagick_1_3" owner="bgruening">
+                        <package name="graphicsmagick" version="1.3.18" />
+                    </repository>
+                </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 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=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
+
+                <!--And finally OSRA 1.4.0-->
+                <action type="shell_command">wget http://share.gruenings.eu/osra-1.4.0-configure.patch</action>
+                <action type="shell_command">patch configure &lt; osra-1.4.0-configure.patch</action>
+                <!-- Extending the PATH is needed for OSRA -->
+                <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp; ./configure --with-tclap-include=$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=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/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 $INSTALL_DIR/cuneiform/ -r</action>
+
+                <action type="set_environment">
+                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$GRAPHICSMAGICK_ROOT_DIR/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>
+                </action>
+            </actions>
+        </install>
+        <readme>We still have a handfull of requirements</readme>
+    </package>
+</tool_dependency>