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This does work, but it's an ugly workaround
<?xml version="1.0"?>
<tool_dependency>
<package name="libxml2" version="2.9.1">
<repository name="package_libxml2_2_9_1" owner="jankanis" prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="98807f0505f0" />
</package>
<package name="libxslt" version="1.1.28">
<repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
</package>
<package name="zlib" version="1.2.8">
<repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="63a4a902cda2" />
</package>
<package name="blast2html_venv" version="0.2">
<install version="1.0">
<actions>
<action type="set_environment_for_install">
<repository name="package_libxml2_2_9_1" owner="jankanis"
toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="98807f0505f0">
<package name="libxml2" version="2.9.1" />
</repository>
<repository name="package_libxslt_1_1_28" owner="devteam"
toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
<package name="libxslt" version="1.1.28" />
</repository>
<repository name="package_zlib_1_2_8" owner="iuc"
toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="63a4a902cda2">
<package name="zlib" version="1.2.8" />
</repository>
</action>
<action type="setup_virtualenv">
jinja2==2.7.3
six==1.7.2
argparse==1.2.1
</action>
<!-- install lxml manually, as the setup_virtualenv action does not include the environment
from set_environment_for_install but shell_command does -->
<action type="shell_command">
$INSTALL_DIR/venv/bin/pip install lxml==3.3.5
</action>
<action type="set_environment">
<!-- add libxml2/zlib library paths so the runtime can find the shared libraries -->
<environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
</action>
</actions>
</install>
<readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
</package>
</tool_dependency>
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