Mercurial > repos > jeremie > package_pindel_0_2_5

diff tool_dependencies.xml @ 2:754f6ec017f7 draft

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author jeremie
date Thu, 19 Jun 2014 08:56:14 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jun 19 08:56:14 2014 -0400
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="samtools" version="0.1.18">
+		<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+	</package>
+	<package name="pindel" version="0.2.5">
+		<install version="1.0">
+			<actions>
+				<action type="download_by_url">https://github.com/genome/pindel/archive/master.zip</action>
+				<action type="shell_command">unzip pindel-master.zip -d pindel</action>
+				<action type="shell_command">cd pindel</action>
+				<action type="shell_command">make SAMTOOLS=~/samtools</action>
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+				</action>
+			</actions>
+		</install>
+		<readme>
+		</readme>
+	</package>
+</tool_dependency>