# HG changeset patch
# User jeremie
# Date 1404308729 14400
# Node ID 291c03afa79137130994b38e287bda1a0688c970

Uploaded

diff -r 000000000000 -r 291c03afa791 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jul 02 09:45:29 2014 -0400
@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="breakdancer" version="1.4.4">
+		<install version="1.0">
+			<actions_group>
+				<actions>
+					<action type="shell_command">git clone --recursive https://github.com/genome/breakdancer</action>
+					<!-- <action type="shell_command">git checkout tags/v1.4.4</action> -->
+					<action type="shell_command">mkdir build</action>
+					<action type="change_directory">build</action>
+					<action type="shell_command">cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local</action>
+					<action type="shell_command">make</action>
+					<action type="move_file"><source>bin/breakdancer-max</source><destination>$INSTALL_DIR/bin</destination></action>
+					<action type="move_file"><source>../perl/bam2cfg.pl</source><destination>$INSTALL_DIR/bin</destination></action>
+					<action type="move_file"><source>../perl/AlnParser.pm</source><destination>$INSTALL_DIR/bin</destination></action>
+					<action type="shell_command">wget https://raw.githubusercontent.com/ALLBio/allbiotc2/master/breakdancer/breakdancer2vcf.py</action>
+					<action type="move_file"><source>breakdancer2vcf.py</source><destination>$INSTALL_DIR/bin</destination></action>
+					<action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
+					<action type="set_environment"><environment_variable name="BREAKDANCER_BIN" action="set_to">$INSTALL_DIR/bin</environment_variable></action>
+				</actions>                     
+			</actions_group>
+		</install>
+		<readme>
+		</readme>
+	</package>
+</tool_dependency>
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