# HG changeset patch
# User devteam
# Date 1387218560 18000
# Node ID ef435b7b0420aea65d0a56e8a74061a169979b6c
# Parent  e21073b0dc1f1ee12e54cef96589124b40e2c7fe
Uploaded updated tool dependency definition.

diff -r e21073b0dc1f -r ef435b7b0420 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 11 15:41:19 2013 -0500
+++ b/tool_dependencies.xml	Mon Dec 16 13:29:20 2013 -0500
@@ -1,47 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
-        <install version="1.0">
-            <actions>
-                <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
-                <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
-                <action type="shell_command">git submodule update --recursive</action>
-                <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
-                <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-FreeBayes requires g++ and the standard C and C++ development libraries.
-Additionally, cmake is required for building the BamTools API.
-        </readme>
+        <repository changeset_revision="102fc9b0884c" name="package_freebayes_0_9_6_9608597d" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>