Mercurial > repos > malbuquerque > delly

diff tool_dependencies.xml @ 39:1e5b1f1b46c1 draft default tip

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author malbuquerque
date Tue, 20 Jan 2015 19:36:31 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jan 20 19:36:31 2015 -0500
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<tool_dependency>
+		
+		<package name="boost" version="1.53.0">
+			<repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+		</package>
+
+		<package name="bamtools" version="2.3.0">
+			<repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+		</package>
+
+		<package name="seqtk" version="1.0.0">
+			<repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+		</package>
+			
+		<package name="delly" version="0.6.1">
+			<install version="1.0">
+				<actions>
+					<action type="set_environment_for_install">
+						<repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+							<package name="boost" version="1.53.0" />
+						</repository>
+					</action>
+					
+					<action type="set_environment_for_install">
+						<repository changeset_revision="ad46b5210186" name="package_bamtools_2_3_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
+							<package name="bamtools" version="2.3.0" />
+						</repository>
+					</action>
+					
+					<action type="set_environment_for_install">
+						<repository changeset_revision="35f0f4568ded" name="package_seqtk_1_0_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu">
+							<package name="seqtk" version="1.0.0" />
+						</repository>
+					</action>
+					
+					<action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
+					<action type="shell_command">pwd &gt; ~/delly.pwd.txt</action>
+					<action type="shell_command">echo $INSTALL_DIR &gt; ~/delly.dir.txt</action>
+					<action type="shell_command">sleep 25</action>
+					<action type="shell_command">make -f $REPOSITORY_INSTALL_DIR/Makefile all BOOST_ROOT=$BOOST_ROOT_DIR/ BAMTOOLS_ROOT=$BAMTOOLS_ROOT/ SEQTK_ROOT=$SEQTK_ROOT/</action>
+					<action type="move_directory_files">
+						<source_directory>.</source_directory>
+						<destination_directory>$INSTALL_DIR</destination_directory>
+					</action>	
+					<action type="set_environment">
+						<environment_variable action="set_to" name="DELLY_DIR">$INSTALL_DIR</environment_variable>
+					</action>
+				</actions>
+			</install>
+		</package>
+
+	</tool_dependency>