diff tool_dependencies.xml @ 12:92ac3fa57a7e draft

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

--- a/tool_dependencies.xml	Thu Aug 27 08:20:09 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 28 07:44:44 2015 -0400
@@ -1,9 +1,5 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <!--<package name="python" version="2.7">
-        <repository name="package_python_2_7" owner="iuc" prior_installation_required="True" />
-    </package>-->
-    
     <package name="nose" version="1.3.7">
         <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
@@ -13,7 +9,7 @@
     </package>
     
     <package name="cython" version="0.23.1">
-        <repository changeset_revision="226a91b737f9" name="package_cython_0_23_1" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1c30e09f01a5" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="crossmap" version="0.2">
@@ -22,15 +18,10 @@
                 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
                 
                 <action type="setup_python_environment">
-                    <!--
-                    <repository name="package_python_2_7" owner="iuc">
-                        <package name="python" version="2.7" />
-                    </repository>
-                    -->
                     <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="nose" version="1.3.7" />
                     </repository>
-                    <repository changeset_revision="226a91b737f9" name="package_cython_0_23_1" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="1c30e09f01a5" name="package_cython_0_23_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="cython" version="0.23.1" />
                     </repository>
                     <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
@@ -38,26 +29,29 @@
                     </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">
-                    which python ; 
+                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
                     
-                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "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;
+                    -->
                     
-                    echo $PYTHONPATH ; 
-                    
-                    python setup.py install --root $INSTALL_DIR
+                    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">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
+                    <environment_variable action="prepend_to" name="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="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>