# HG changeset patch
# User dpryan79
# Date 1473765698 14400
# Node ID cbb49b5bc43fdde9b2ab8b0b55d763ef49f9db32

Uploaded

diff -r 000000000000 -r cbb49b5bc43f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 13 07:21:38 2016 -0400
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bwa" version="0.7.12">
+        <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bwameth" version="0.20">
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                    <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+                </action>
+                <action type="shell_command">git clone https://github.com/brentp/bwa-meth</action>
+                <action type="shell_command">git reset --hard 7dfec747105b9fa2cf1678bf5f67e860a0155d0e</action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
+             </actions>
+         </install>
+         <readme>
+            Installation of bwa-meth from Brent Pedersen
+            https://github.com/brentp/bwa-meth
+         </readme>
+     </package>
+</tool_dependency>