# HG changeset patch
# User geert-vandeweyer
# Date 1392301618 18000
# Node ID 528af4b27a3ebcae465c72bb55b122110387b124
# Parent  b3afcf0d6d2c4aad6f4bb14b76b4e1cdc382855a
Uploaded

diff -r b3afcf0d6d2c -r 528af4b27a3e tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Feb 13 09:26:48 2014 -0500
+++ b/tool_dependencies.xml	Thu Feb 13 09:26:58 2014 -0500
@@ -1,13 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="perl_module_threads" version="1.92">
-        <repository changeset_revision="01ed0b079724" name="package_perl_threading" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl_module_threads_shared" version="1.46">
-        <repository changeset_revision="01ed0b079724" name="package_perl_threading" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="MUTECT_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable>
+    </set_environment>
+   <package name="samtools" version="0.1.18">
+        <repository changeset_revision="a7936f4ea405" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="perl_module_Thread_Queue" version="3.02">
-        <repository changeset_revision="01ed0b079724" name="package_perl_threading" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-
-</tool_dependency>
+</tool_dependency>