diff tool_dependencies.xml @ 2:00d73c812399 draft

Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2.

--- a/tool_dependencies.xml	Tue Jul 26 10:34:49 2016 -0400
+++ b/tool_dependencies.xml	Wed Mar 22 11:36:07 2017 -0400
@@ -8,7 +8,7 @@
     <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <!-- Subset of UCSC tools -->
-  <package name="ucsc_tools_for_macs21" version="1.0">
+  <package name="ucsc_tools_for_macs21" version="2.0">
       <install version="1.0">
             <actions>
 	      <!-- fetchChromSizes -->
@@ -25,6 +25,13 @@
               <action type="chmod">
                 <file mode="755">$INSTALL_DIR/bedClip</file>
               </action>
+	      <!-- bedSort -->
+              <action type="download_binary">
+                <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedSort</url_template>
+              </action>
+              <action type="chmod">
+                <file mode="755">$INSTALL_DIR/bedSort</file>
+              </action>
 	      <!-- bedGraphToBigWig -->
               <action type="download_binary">
                 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>