Mercurial > repos > malbuquerque > package_bamtools_2_3_0

diff tool_dependencies.xml @ 0:2c55ff0a3013 draft

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author malbuquerque
date Mon, 19 Jan 2015 18:52:05 -0500
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children 38dafb8b3980
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 19 18:52:05 2015 -0500
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool_dependency>
+
+		<package name="cmake" version="3.1.0">
+			<repository changeset_revision="a18ccb33a785" name="package_cmake_3_1_0" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
+		</package>
+
+		<package name="samtools" version="0.1.18">
+			<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+		</package>
+	
+		<package name="bamtools" version="2.3.0">
+			<install version="1.0">
+				<actions>
+
+					<action type="download_by_url">https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz</action>
+					<action type="shell_command">mkdir build</action>
+					<action type="shell_command">cd build</action>
+					<action type="shell_command">cmake ..</action>
+					<action type="shell_command">make</action>
+					<action type="shell_command">cd ..</action>
+
+					<action type="move_directory_files">
+						<source_directory>./</source_directory>
+						<destination_directory>$INSTALL_DIR</destination_directory>
+					</action>
+
+					<action type="set_environment">
+						<environment_variable action="set_to" name="BAMTOOLS_ROOT">$INSTALL_DIR</environment_variable>
+						<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+					</action>
+
+				</actions>	
+			</install>
+		</package>
+
+	</tool_dependency>