diff tool_dependencies.xml @ 21:c46406466625 draft

Uploaded
author wolma
date Sat, 11 Jun 2016 19:10:44 -0400
parents aba6d9b1c1f1
children 24154c580718
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--- a/tool_dependencies.xml	Fri Apr 29 06:01:46 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 11 19:10:44 2016 -0400
@@ -4,13 +4,13 @@
     <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="R" version="3.2.1">
-    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="readline" version="6.3">
     <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="python3" version="3.4">
-    <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
     
   <package name="mimodd" version="0.1.7.2">
@@ -18,7 +18,7 @@
       <actions>
       <!-- prepare a python3 venv to install into -->
         <action type="set_environment_for_install">
-          <repository changeset_revision="5e5653b689ca" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
+          <repository changeset_revision="83407422ec16" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="python3" version="3.4" />
           </repository>
         </action>
@@ -50,7 +50,7 @@
           <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="readline" version="6.3" />
           </repository>
-          <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+          <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
             <package name="R" version="3.2.1" />
           </repository>
         </action>
@@ -77,8 +77,11 @@
         
       <!-- configure environment -->
         <action type="set_environment">
-          <!-- make the mimodd entry script discoverable -->
-          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
+          <!-- to make MiModD accessible it is sufficient to simply add the 
+               venvs site-packages directory to PYTHONPATH; 
+               SITE_PACKAGES_RELPATH will be made available by the python3 
+               package, which all MiModD toolwrappers require -->
+          <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/MiModD_venv/$SITE_PACKAGES_RELPATH</environment_variable>
         </action>
       </actions>
     </install>