Mercurial > repos > yhoogstrate > package_segmentation_fold_1_6_2

changeset 2:c8495f2ee9bd draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 3d4c8888c2257e2c01255ea4141fe96bcf6960df-dirty
author yhoogstrate
date Wed, 02 Mar 2016 09:46:53 -0500
parents 34af794144dc
children 60f5061f5116
files tool_dependencies.xml
diffstat 1 files changed, 23 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Mar 02 05:30:54 2016 -0500
+++ b/tool_dependencies.xml	Wed Mar 02 09:46:53 2016 -0500
@@ -8,6 +8,10 @@
         <repository changeset_revision="2da7b99cb1a1" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    
     <package name="segmentation-fold" version="1.6.2">
         <install version="1.0">
             <actions>
@@ -32,9 +36,25 @@
                     make install
                 </action>
                 
+                <!-- Also install the python utils -->
+                <action type="set_environment_for_install">
+                     <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python  &amp;&amp;
+                    python ./scripts/energy-estimation-utility/setup.py
+                        --home $INSTALL_DIR
+                        --install-scripts $INSTALL_DIR/bin
+                </action>
+                
                 <action type="set_environment">
-                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                     <environment_variable action="set_to" name="SEGMENTATION_FOLD_DEFAULT_XML">$INSTALL_DIR/share/segmentation-fold/segments.xml</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="SEGMENTATION_FOLD_DEFAULT_XML">$INSTALL_DIR/share/segmentation-fold/segments.xml</environment_variable>
                 </action>
             </actions>
         </install>
@@ -43,6 +63,7 @@
              - libboost                     (via toolshed)
              - CMake                        (via toolshed)
              - c++11 compliant compiler: g++ or clang
+             - Python (for energy utils)
         </readme>
     </package>
 </tool_dependency>