# HG changeset patch
# User dpryan79
# Date 1473852278 14400
# Node ID 435f9d24c0603d1d331d86c1ab692c12d8e53daf
# Parent  831f8397a4242d261d83a5ca846589182adc1f37
Uploaded

diff -r 831f8397a424 -r 435f9d24c060 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 13 08:00:06 2016 -0400
+++ b/tool_dependencies.xml	Wed Sep 14 07:24:38 2016 -0400
@@ -1,13 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <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="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" />
+       <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" 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" />
+       <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" 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 name="toolshed" version="0.4.6">
+       <repository changeset_revision="c0ca6d5a5c5c" name="package_python_2_7_toolshed_0_4_6" owner="dpryan79" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bwameth" version="0.20">
         <install version="1.0">
@@ -16,18 +19,17 @@
                     <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>
+                    <package md5sum="7d6e2ed375da0fc3d44de3477aa5c087">https://github.com/brentp/bwa-meth/archive/v0.2.0.tar.gz</package>
                 </action>
                 <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$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">git clone https://github.com/brentp/bwa-meth &amp;&amp; cd bwa-meth &amp;&amp; git reset --hard 7dfec747105b9fa2cf1678bf5f67e860a0155d0e &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
+            Installation of toolshed from Brent Pedersen
+            https://github.com/brentp/toolshed
          </readme>
      </package>
 </tool_dependency>