# HG changeset patch
# User pjbriggs
# Date 1520262828 18000
# Node ID dfa082f8406890453da9d7966379f38e5fc224f1
# Parent  53af7b5b1b569a2e33689d795d36f09ad9893c2b
Uploaded version 0.36.5 (use conda to resolve tool dependencies)

diff -r 53af7b5b1b56 -r dfa082f84068 README.rst
--- a/README.rst	Mon Aug 21 04:59:09 2017 -0400
+++ b/README.rst	Mon Mar 05 10:13:48 2018 -0500
@@ -71,6 +71,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
+0.36.5     - Remove tool_dependencies.xml and always use conda to resolve tool
+             dependencies
 0.36.4     - Add option to provide custom adapter sequences for ILLUMINACLIP
            - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP
              in palindrome mode
diff -r 53af7b5b1b56 -r dfa082f84068 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 21 04:59:09 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="trimmomatic" version="0.36">
-      <install version="1.0">
-	<actions>
-	  <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
-	  <action type="move_file" rename_to="trimmomatic.jar">
-	    <source>trimmomatic-0.36.jar</source>
-	    <destination>$INSTALL_DIR</destination>
-	  </action>
-          <action type="move_directory_files">
-            <source_directory>adapters</source_directory>
-            <destination_directory>$INSTALL_DIR/adapters</destination_directory>
-          </action>
-	  <action type="set_environment">
-	    <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-	  </action>
-	  <action type="set_environment">
-	    <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable>
-	  </action>
-	</actions>
-      </install>
-      <readme>Trimmomatic requires the Java Runtime Environment
-      </readme>
-    </package>
-</tool_dependency>
-
diff -r 53af7b5b1b56 -r dfa082f84068 trimmomatic.xml
--- a/trimmomatic.xml	Mon Aug 21 04:59:09 2017 -0400
+++ b/trimmomatic.xml	Mon Mar 05 10:13:48 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.36.4">
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.5">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <macros>
     <import>trimmomatic_macros.xml</import>