# HG changeset patch
# User Ilya Sytchev <isytchev@hsph.harvard.edu>
# Date 1381869232 14400
# Node ID e047d7bbace9a1f8c3640c49f4a2aff0ee21c7a7
# Parent  14f378e351913161e9a1deaf07458278e538c46c
Remove MACS2 external dependency.  Change tool name and version number.

diff -r 14f378e35191 -r e047d7bbace9 macs2_wrapper.xml
--- a/macs2_wrapper.xml	Fri Jan 25 11:49:55 2013 -0500
+++ b/macs2_wrapper.xml	Tue Oct 15 16:33:52 2013 -0400
@@ -1,9 +1,4 @@
-<tool id="modencode_peakcalling_macs2" name="MACS2" version="2.0.10.2">
-  <requirements>
-    <requirement type="python-module">macs2</requirement>
-    <requirement type="package" version="2.0.10.2">macs2</requirement>
-    <!--<requirement type="set_environment">SCRIPT_PATH</requirement>-->
-  </requirements>
+<tool id="macs2_peakcalling" name="MACS2" version="2.0.10">
   <description>Model-based Analysis of ChIP-Seq</description>
   <command interpreter="python">macs2_wrapper.py $options_file $outputs_file</command>
   <inputs>
@@ -230,4 +225,4 @@
 
 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
   </help>
-</tool>
\ No newline at end of file
+</tool>
diff -r 14f378e35191 -r e047d7bbace9 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jan 25 11:49:55 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="macs2" version="2.0.10.2">
-        <install version="1.0">           
-            <!--<actions>
-                <action type="download_by_url">http://data.modencode.org/modENCODE_Galaxy/tarballs/Python-2.7.3.tar.bz2</action>
-                <action type="shell_command">./configure</action>
-                <action type="shell_command">make -j</action>
-                <action type="shell_command">sudo -n make install</action>
-                <action type="shell_command">sudo -n chmod ag+w /usr/local/lib/python2.7/site-packages</action>
-                <action type="shell_command">sudo -n chmod ag+wx /usr/local/bin</action>
-            </actions>-->
-            <actions>
-                <action type="download_by_url">http://data.modencode.org/modENCODE_Galaxy/tarballs/macs2pkg.tar</action>
-                <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                </action>
-                <action type="move_directory_files">
-                    <source_directory>lib</source_directory>
-                    <destination_directory>$INSTALL_DIR/lib</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Macs2 depends on having python2.7 installed on all nodes of the work cluster</readme>
-    </package>
-</tool_dependency>
-
-<!--<action type="download_by_url">http://data.modencode.org/modENCODE_Galaxy/tarballs/numpy.tar</action>
-                <action type="shell_command">sudo -n python setup.py build</action>
-                <action type="shell_command">sudo -n python setup.py install</action>-->
-