view tool_dependencies.xml @ 22:5e5611bc7497 draft

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<?xml version="1.0"?>
<tool_dependency>
	
	<set_environment version="1.0">
     	<environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

	<package name="R" version="3.0.3">
		<repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
	</package>
	
	<package name="bioc_qdnaseq" version="1.0.5">
		<install version="1.0">
			<actions>
				<action type="shell_command">echo "[DEBUG] INSTALL DIR: $INSTALL_DIR"</action>
				<action type="shell_command">echo "[DEBUG] REPOS INSTALL DIR: $REPOSITORY_INSTALL_DIR"</action>
				
				<action type="shell_command">echo "[DEBUG] BEFORE:" &amp;&amp; pwd</action>
				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
				<action type="shell_command">echo "[DEBUG] DIR LISTING ONE UP:" &amp;&amp; ls -l ../</action>
				<!--
				<action type="move_file">
					<source>../QDNAseq.R</source>
					<destination>./</destination>
				</action>
				-->
				
				<action type="shell_command">echo "[DEBUG] AFTER:" &amp;&amp; pwd</action>
				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>

				<action type="set_environment_for_install">
					<repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
						<package name="R" version="3.0.3" />
					</repository>
				</action>
				<action type="set_environment">
						<environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
				</action>
				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action>
				
				<action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
				
				<action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
				<action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
				
				<action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action>
				<!--
<action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL --> <!--build QDNAseq_1.0.5.tar.gz</action>
				-->
				<!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>-->
			</actions>
		</install>
		
		<readme>
			Should install QDNAseq package from bioconductor.
		</readme>
	</package>
		
</tool_dependency>