# HG changeset patch
# User nml
# Date 1467913394 14400
# Node ID af0cf1f508fa98997695d99e84e2d5e8dd4d5180
# Parent  38541eaf0d2012c4a4398199434a52c213742f35
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty

diff -r 38541eaf0d20 -r af0cf1f508fa tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jul 07 09:58:46 2016 -0400
+++ b/tool_dependencies.xml	Thu Jul 07 13:43:14 2016 -0400
@@ -6,8 +6,8 @@
     <package name="cmake" version="3.2.3">
       <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" 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="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="pysam" version="0.8.3">
         <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -19,13 +19,19 @@
       <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bioext" version="0.17.3">
-      <repository changeset_revision="d71e21675123" name="package_python_3_4_bioext_0_17_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+      <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="cython" version="0.23.4">
+      <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="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="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="hivclustering" version="1.2.3">
-      <repository changeset_revision="594976628691" name="package_python_3_4_hivclustering_1_2_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="eda1cbde6572" name="package_python_3_4_hivclustering_1_2_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="tn93" version="1.0.2">
       <repository changeset_revision="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -35,8 +41,8 @@
           <actions>
             <action type="download_by_url">https://github.com/veg/hivtrace/archive/0.1.4.tar.gz</action>
             <action type="set_environment_for_install">
-                <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="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                     <package name="pysam" version="0.8.3" />
@@ -47,12 +53,21 @@
                 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                     <package name="biopython" version="1.66" />
                 </repository>
-                <repository changeset_revision="d71e21675123" name="package_python_3_4_bioext_0_17_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                <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="594976628691" name="package_python_3_4_hivclustering_1_2_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                <repository changeset_revision="eda1cbde6572" name="package_python_3_4_hivclustering_1_2_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                     <package name="hivclustering" version="1.2.3" />
                 </repository>
+                <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="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="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="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                     <package name="tn93" version="1.0.2" />
                 </repository>
@@ -76,6 +91,11 @@
               <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOEXT]</environment_variable>
               <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
               <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
+              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HYPHY_PYTHON]</environment_variable>
+              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_CYTHON]</environment_variable>
+              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HIVCLUSTERING]</environment_variable>
+              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_FAKEMP]</environment_variable>
+              <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HPPY]</environment_variable>
               <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
               <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
               <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>