Mercurial > repos > big-tiandm > degseq

view tool_dependencies.xml @ 21:94bc6d663e36 draft

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author big-tiandm
date Sat, 15 Nov 2014 00:58:54 -0500
parents 32970aaa6af8
children b5b3d44170ca
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<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

	<package name="R" version="3.0.1">
	   <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True"/>

		<install version="1.0">
		   <actions>
		      <action type="set_environment_for_install">
                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" prior_installation_required="True">
                        <package name="R" version="3.0.1" />
                    </repository>
              </action>
		      <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
		      <action type="shell_command">RPATH=`which R`</action>
  		      <action type="shell_command">echo "export PATH=$RPATH:$PATH" \> $INSTALL_DIR/env.sh </action>
			  <action type="shell_command">chmod 755 SINSTALL_DIR/env.sh </action>

		 </actions>
		</install>
	</package>


</tool_dependency>