# HG changeset patch
# User devteam <devteam@galaxyproject.org>
# Date 1389635238 18000
# Node ID dc82017052acadf060d17bb24db97171cd8751c3
# Parent  2a846521018aef710b849506bf10bd18dd9687b7# Parent  dfd39244354fea0a8a2b9a2aac25d3aff497e427
Merge heads at 77:dfd39244354f and 78:2a846521018a which were created as a result of a recently fixed bug.

diff -r 2a846521018a -r dc82017052ac repository_dependencies.xml.pre-commit-backup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml.pre-commit-backup	Mon Jan 13 12:47:18 2014 -0500
@@ -0,0 +1,4 @@
+<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
+    <repository name="molecule_datatypes" owner="bgruening"  />
+    
+</repositories>
diff -r 2a846521018a -r dc82017052ac tool_dependencies.xml
diff -r 2a846521018a -r dc82017052ac tool_dependencies.xml.pre-commit-backup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.pre-commit-backup	Mon Jan 13 12:47:18 2014 -0500
@@ -0,0 +1,64 @@
+<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="2.0.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
+
+                <action type="set_environment_for_install">
+                    <repository name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="openbabel" version="2.3.2" />
+                    </repository>
+                    <repository name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="graphicsmagick" version="1.3.18" />
+                    </repository>
+                </action>
+                <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=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
+
+                <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
+                <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
+
+
+                
+                <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=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
+
+                
+                <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
+                <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
+
+                
+                <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=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
+
+                
+                
+                <action type="shell_command">export PATH=$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/gocr/ -r</action>
+                <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action>
+                <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$GRAPHICSMAGICK_ROOT_DIR/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>