# HG changeset patch
# User nml
# Date 1467899926 14400
# Node ID 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

diff -r 000000000000 -r 38541eaf0d20 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 07 09:58:46 2016 -0400
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="3.4">
+      <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <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>
+    <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" />
+    </package>
+    <package name="numpy" version="1.10.1">
+      <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="biopython" version="1.66">
+      <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" />
+    </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" />
+    </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" />
+    </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" />
+    </package>
+    <package name="hivtrace" version="0.1.4">
+        <install version="1.0">
+          <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>
+                <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" />
+                </repository>
+                <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <package name="numpy" version="1.10.1" />
+                </repository>
+                <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">
+                    <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">
+                    <package name="hivclustering" version="1.2.3" />
+                </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>
+                <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>
+            </action>
+            <action type="make_directory">$INSTALL_DIR/lib/python</action>
+            <action type="make_directory">$INSTALL_DIR/bin</action>
+            <action type="shell_command">
+              ln -s $PATH_PYTHON3/python3 $INSTALL_DIR/bin/python3 &amp;&amp;
+              export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+              export PATH=$PATH:$PATH_NUMPY &amp;&amp;
+              export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
+              $INSTALL_DIR/bin/python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+            </action>
+            <action type="set_environment">
+              <environment_variable action="append_to" name="PYTHONPATH">$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_BIOPYTHON]</environment_variable>
+              <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">$ENV[PYTHONPATH_PYSAM]</environment_variable>
+              <environment_variable action="prepend_to" name="PATH">$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>
+              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_HIVCLUSTERING]</environment_variable>
+              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BIOEXT]</environment_variable>
+              <environment_variable action="prepend_to" name="PATH">$ENV[PATH_TN93]</environment_variable>
+            </action>
+          </actions>
+        </install>
+        <readme>
+This installs hivtrace 0.1.4 (and all its dependencies).
+
+See usage instructions here: https://github.com/veg/hivtrace
+        </readme>
+    </package>
+</tool_dependency>