Mercurial > repos > yhoogstrate > package_crossmap_0_2

diff tool_dependencies.xml @ 13:b12b628ee597 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty
author yhoogstrate
date Fri, 28 Aug 2015 07:53:20 -0400
parents 92ac3fa57a7e
children d7af71949bef
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--- a/tool_dependencies.xml	Fri Aug 28 07:44:44 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 28 07:53:20 2015 -0400
@@ -38,15 +38,15 @@
                 <action type="shell_command">
                     sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
                     
+                    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 $INSTALL_DIR/lib
+                    
                     <!--
                     export PYTHONPATH="$CYTHON_PATH/lib:$PYTHONPATH" &amp;&amp;
                     export PYTHONPATH="$CYTHON_PATH/lib/python:$PYTHONPATH" &amp;&amp;
                     export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
                     -->
-                    
-                    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">
@@ -54,7 +54,7 @@
                     <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="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
+                    <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
                     <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>