# HG changeset patch
# User nml
# Date 1467912848 14400
# Node ID eda1cbde6572403ed231a5ce3bf7388899e0d15a
# Parent  5b977873cc872ac281cc2447ec0b3de26f13d775
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivclustering_1_2_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty

diff -r 5b977873cc87 -r eda1cbde6572 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jul 07 11:19:37 2016 -0400
+++ b/tool_dependencies.xml	Thu Jul 07 13:34:08 2016 -0400
@@ -6,32 +6,38 @@
         <package name="bioext" version="0.17.3">
           <repository changeset_revision="1ca9f5fd8b65" name="package_python_3_4_bioext_0_17_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
         </package>
-        <package name="hyphy" version="2.2.6">
-          <repository changeset_revision="6e10967fdc7a" name="package_python_3_4_hyphy_2_2_6" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <package name="fakemp" version="0.9.1">
+          <repository changeset_revision="13da2754601c" name="package_python_3_4_fakemp_0_9_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        </package>
+        <package name="hyphy-python" version="0.1.3">
+          <repository changeset_revision="5c14a49141f0" name="package_python_3_4_hyphy_python_0_1_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
         </package>
         <package name="hppy" version="0.9.6">
-          <repository changeset_revision="ded93000c5da" name="package_python_3_4_hppy_0_9_6" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+          <repository changeset_revision="46decde5b780" name="package_python_3_4_hppy_0_9_6" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
         </package>
         <package name="cython" version="0.23.4">
-          <repository changeset_revision="c065e365766c" name="package_python_3_4_cython_0_23_4" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+          <repository changeset_revision="52c11d398790" name="package_python_3_4_cython_0_23_4" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
         </package>
         <package name="hivclustering" version="1.2.3">
             <install version="1.0">
                 <actions>
                     <action type="download_by_url">https://github.com/veg/hivclustering/archive/1.2.3.tar.gz</action>
                     <action type="set_environment_for_install">
-                        <repository changeset_revision="c065e365766c" name="package_python_3_4_cython_0_23_4" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="52c11d398790" name="package_python_3_4_cython_0_23_4" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="cython" version="0.23.4" />
                         </repository>
-                        <repository changeset_revision="6e10967fdc7a" name="package_python_3_4_hyphy_2_2_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
-                            <package name="hyphy" version="2.2.6" />
+                        <repository changeset_revision="5c14a49141f0" name="package_python_3_4_hyphy_python_0_1_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="hyphy-python" version="0.1.3" />
                         </repository>
-                        <repository changeset_revision="ded93000c5da" name="package_python_3_4_hppy_0_9_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <repository changeset_revision="46decde5b780" name="package_python_3_4_hppy_0_9_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="hppy" version="0.9.6" />
                         </repository>
                         <repository changeset_revision="1ca9f5fd8b65" name="package_python_3_4_bioext_0_17_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="bioext" version="0.17.3" />
                         </repository>
+                        <repository changeset_revision="13da2754601c" name="package_python_3_4_fakemp_0_9_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="fakemp" version="0.9.1" />
+                        </repository>
                         <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                             <package name="python" version="3.4" />
                         </repository>
@@ -43,9 +49,14 @@
                     </action>
                     <action type="set_environment">
                       <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                      <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOEXT]</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_FAKEMP]</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HYPHY_PYTHON]</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HPPY]</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_CYTHON]</environment_variable>
                       <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                       <environment_variable action="set_to" name="PATH_HIVCLUSTERING">$INSTALL_DIR/bin</environment_variable>
+                      <environment_variable action="set_to" name="PYTHONPATH_HIVCLUSTERING">$INSTALL_DIR/lib/python</environment_variable>
                     </action>
                 </actions>
             </install>