# HG changeset patch
# User nml
# Date 1467899867 14400
# Node ID d71e216751230ad7ba99277f51bcd6e791b5021d

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_bioext_0_17_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa

diff -r 000000000000 -r d71e21675123 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 07 09:57:47 2016 -0400
@@ -0,0 +1,55 @@
+<?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="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">
+            <install version="1.0">
+                <actions>
+                    <action type="download_by_url">https://github.com/veg/BioExt/archive/0.17.3.tar.gz</action>
+                    <action type="set_environment_for_install">
+                        <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="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">$INSTALL_DIR/lib/python</action>
+                    <action type="shell_command">
+                      export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                      export PATH=$PATH:$PATH_NUMPY &amp;&amp;
+                      export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
+                      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</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                      <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
+                      <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                      <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                      <environment_variable action="set_to" name="PYTHONPATH_BIOEXT">$INSTALL_DIR/lib/python</environment_variable>
+                      <environment_variable action="set_to" name="PATH_BIOEXT">$INSTALL_DIR/bin</environment_variable>
+                    </action>
+                </actions>
+            </install>
+            <readme>A few handy bioinformatics tools not already within BioPython</readme>
+        </package>
+</tool_dependency>