# HG changeset patch
# User yhoogstrate
# Date 1446649888 18000
# Node ID e4de7f1284ce1fda9bc175334e9fc94da024f726
# Parent  803db5577b07694e9249d0106cd24db6456e278c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7

diff -r 803db5577b07 -r e4de7f1284ce tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 28 03:43:49 2015 -0400
+++ b/tool_dependencies.xml	Wed Nov 04 10:11:28 2015 -0500
@@ -5,7 +5,7 @@
     </package>
     
     <package name="numpy" version="1.9">
-        <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="cython" version="0.23.1">
@@ -24,30 +24,31 @@
                     <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="cython" version="0.23.1" />
                     </repository>
-                    <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.9" />
                     </repository>
                 </action>
                 
-                <!-- CrossMap doesn't pick up the correct Cython path.
-                Therefore install it with a manual shell_command instead
-                of <package></package> inside a pyton_env. -->
+                <!-- If CrossMap is installed with - - home or - - prefix
+                into, it often crashes with a 'write-test' error
+                
+                Using - - root places the installation in:
+                $INSTALL_DIR / (python path dir) /
+                -->
                 <action type="shell_command">
-                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
+                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
                     
-                    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
+                    python setup.py install --root $INSTALL_DIR &amp;&amp;
+                    export SUB_DIR=$(dirname $(which python)) &amp;&amp;
+                    mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
+                    mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin
                 </action>
                 
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/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>