diff tool_dependencies.xml @ 17:823f0b1beccd draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty

--- a/tool_dependencies.xml	Fri Aug 28 07:59:01 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 28 08:49:15 2015 -0400
@@ -36,26 +36,17 @@
                 $INSTALL_DIR / (python path dir) /
                 -->
                 <action type="shell_command">
-
-                    
-                    echo "a" ; 
-                    echo "b" &amp;&amp;
-                    echo "c" ;
+                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
                     
-                    <!--
-                    comment
-                    -->
-                    
-                    echo "d" ; 
-                    echo "e" &amp;&amp;
-                    echo "f" 
-                    
+                    python setup.py install --root $INSTALL_DIR &amp;&amp;
+                    mv $INSTALL_DIR$(which python)/bin $INSTALL_DIR/bin &amp;&amp;
+                    mv $INSTALL_DIR$(which python)/lib $INSTALL_DIR/lib
                 </action>
                 
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                     <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python"</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                     
                     <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
                     <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>