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changeset 5:42c29d1051e8

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Uploaded
author bgruening
date Thu, 23 May 2013 04:03:55 -0400
parents 9c79d74d23ef
children 035f845a6edc
files tool_dependencies.xml
diffstat 1 files changed, 27 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu May 23 03:36:28 2013 -0400
+++ b/tool_dependencies.xml	Thu May 23 04:03:55 2013 -0400
@@ -1,68 +1,73 @@
-<?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 name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" />
     </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" />
+        <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>
-                
+                <!-- first action is always downloading -->
                 <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
 
-                
+                <!-- 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 name="package_openbabel_2_3" owner="bgruening">
                         <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">
+                    <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 -->
+                <!-- not yet possible 
                 <action type="shell_command">wget http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action>
                 <action type="shell_command">tar xfvz gocr-0.50.tar.gz &amp;&amp; cd gocr-0.50 &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
+                -->
+                <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
+                <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$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>
 
-                
-                
-                <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>
+                <!--And finally OSRA 1.4.0-->
+                <!-- 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 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>
+                    <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>
\ No newline at end of file
+</tool_dependency>