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<?xml version="1.0"?>
<tool_dependency>
  <package name="mutationseq_python_environment" version = "4.3.6">
    <install version="1.0">
      <actions_group>
        <actions os="linux" architecture="x86_64">
          <action type="download_by_url" md5sum="874dbb0d3c7ec665adf7231bbb575ab2" target_filename="Miniconda3-4.1.11-Linux-x86_64.sh">
            https://repo.continuum.io/miniconda/Miniconda3-4.1.11-Linux-x86_64.sh
          </action>
          <action type="shell_command">
            bash Miniconda3-4.1.11-Linux-x86_64.sh -b -f -p $INSTALL_DIR
          </action>
        </actions>
        <actions os="darwin" architecture="x86_64">
          <action type="download_by_url" md5sum="870d6f99eda1263c6e857d637e861d20" target_filename="Miniconda3-4.1.11-MacOSX-x86_64.sh">
            https://repo.continuum.io/miniconda/Miniconda3-4.1.11-MacOSX-x86_64.sh
          </action>
          <action type="shell_command">
            bash Miniconda3-4.1.11-MacOSX-x86_64.sh -b -f -p $INSTALL_DIR
          </action>
        </actions>
        <action type="shell_command">
          $INSTALL_DIR/bin/python $INSTALL_DIR/bin/conda install --quiet python=2.7 numpy=1.7.1 scipy=0.12.0 scikit-learn=0.14.1 matplotlib=1.2.1
        </action>
        <action type="shell_command">
          $INSTALL_DIR/bin/pip install --quiet --ignore-installed --prefix $INSTALL_DIR intervaltree==2.0.4
        </action>
        <action type="set_environment">
	  <environment_variable action="set_to" name="MUTATIONSEQ_PYTHON_ENVIRONMENT_ROOT_DIR">$INSTALL_DIR</environment_variable>
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
        </action>
      </actions_group>
    </install>
  </package>
</tool_dependency>