# HG changeset patch
# User greg
# Date 1502383854 14400
# Node ID 00b59afd9fbd6c3eb2a69215e96aef583f15ee49
# Parent  8c6de654737ba1a62ac27413ed158646b06abe49
Uploaded

diff -r 8c6de654737b -r 00b59afd9fbd ideas.xml
--- a/ideas.xml	Thu Aug 10 12:46:17 2017 -0400
+++ b/ideas.xml	Thu Aug 10 12:50:54 2017 -0400
@@ -9,8 +9,10 @@
     </requirements>
     <command><![CDATA[
 #import os
-#set tmp_dir = ($os.path.join($os.getcwd(), 'tmp')
+#set tmp_dir = $os.path.join($os.getcwd(), 'tmp')
+#set prep_output_dir = $os.path.join($os.getcwd(), 'prep_output')
 mkdir -p $tmp_dir &&
+mkdir -p $prep_output_dir &&
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -67,7 +69,6 @@
 ##############################################
 ## Run IDEAS on the R matrix
 ##############################################
-&& mkdir -p output
 && ideas
 '$build_config_file'
 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
@@ -120,10 +121,10 @@
     -maxerr $set_max_standard_dev_cond.max_standard_dev
 #end if
 -thread \${GALAXY_SLOTS:-4}
--o output
-&& mv output/*.state $output_state
-&& mv output/*.para $output_para
-&& mv output/*cluster $output_cluster
+-o $prep_output_dir
+&& mv $prep_output_dir/*.state $output_state
+&& mv $prep_output_dir/*.para $output_para
+&& mv $prep_output_dir/*cluster $output_cluster
     ]]></command>
     <configfiles>
         <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: