Mercurial > repos > malbuquerque > delly

diff package/tool_dependencies.xml @ 0:ace1798624b4 draft

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author malbuquerque
date Tue, 20 Jan 2015 14:16:43 -0500
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children 5f241f2398c3
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/package/tool_dependencies.xml	Tue Jan 20 14:16:43 2015 -0500
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+		
+		<package name="boost" version="1.53">
+			<repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" 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" 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" toolshed="https://toolshed.g2.bx.psu.edu" />
+		</package>
+			
+		<package name="delly" version="0.6.1">
+			<install version="1.0.0">
+				<actions>
+					<action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
+					<action type="download_by_url">https://github.com/morinlab/galaxy_tools/delly/Makefile</action>
+					<action type="shell_command">make all BOOST_ROOT=\$BOOST_ROOT 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>