Mercurial > repos > morinlab > package_bamtools_2_3_0

diff tool_dependencies.xml @ 0:17def8636dd4 draft default tip

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/packages/package_bamtools_2_3_0 commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 13:34:22 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 11 13:34:22 2016 -0400
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="cmake" version="3.1.0">
+		<repository changeset_revision="e9baec7e0438" name="package_cmake_3_1_0" owner="morinlab" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	</package>
+	<package name="samtools" version="0.1.18">
+		<repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.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="set_environment_for_install">
+					<repository changeset_revision="e9baec7e0438" name="package_cmake_3_1_0" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="cmake" version="3.1.0" />
+					</repository>
+				</action>
+
+				<action type="set_environment_for_install">
+					<repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="samtools" version="0.1.18" />
+					</repository>
+				</action>		
+	
+				<action type="shell_command">mkdir build</action>
+				<action type="change_directory">build</action>
+				<action type="shell_command">cmake ..</action>
+				<action type="shell_command">make</action>
+				<action type="change_directory">..</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>