annotate tool_dependencies.xml @ 0:b8d22acd3017 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_pysam_0_8_2 commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty

<?xml version="1.0"?>
<tool_dependency>
	<package name="ez_setup" version="0.9">
		<!--
			If cross-toolshed depenencies become allowed use the following:
			<repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
		-->
		<repository changeset_revision="10fd2e2a9f2f" name="package_ez_setup_0_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
	</package>
	
	<package name="pysam" version="0.8.2.1">
		<install version="1.0">
			<actions>
				<action md5sum="daf63c1665fa601fc942f050f334a627" type="download_by_url">https://pypi.python.org/packages/source/p/pysam/pysam-0.8.2.1.tar.gz</action>
				<action type="set_environment_for_install">
					<!--
						If cross-toolshed depenencies become allowed use the following:
						<repository changeset_revision="f50b27b88d30" name="package_ez_setup_0_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
					-->
					<repository changeset_revision="10fd2e2a9f2f" name="package_ez_setup_0_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
						<package name="ez_setup" version="0.9" />
					</repository>
				</action>
				<action type="make_directory">$INSTALL_DIR/lib/python</action>
				<action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
				<action type="set_environment">
					<environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
					<environment_variable action="set_to" name="PYSAM_PATH">$INSTALL_DIR</environment_variable>
					<environment_variable action="set_to" name="PYSAM_ROOT_PATH">$INSTALL_DIR</environment_variable>
				</action>
			</actions>
		</install>
		<readme>
			Installation of pysam, pyrex and python are required. The installation can be accessed via PYSAM_PATH.
			The PYSAM_PATH has to be within the PYTHONPATH to let python automatically load this library.
		</readme>
	</package>
</tool_dependency>