# HG changeset patch
# User greg
# Date 1502715778 14400
# Node ID 0cf1998634007299509a4316c73c6b0fac1b1948
# Parent  53891e4e4c6343013fd1c97aee4cf826e2bdca23
Uploaded

diff -r 53891e4e4c63 -r 0cf199863400 ideas.xml
--- a/ideas.xml	Mon Aug 14 08:31:13 2017 -0400
+++ b/ideas.xml	Mon Aug 14 09:02:58 2017 -0400
@@ -11,12 +11,10 @@
     <command><![CDATA[
 #import os
 #set tmp_dir = 'tmp'
-#set prep_output_dir = 'prep_output'
 #set prep_output_config = 'prep_output_config.txt'
-#set ideas_input_dir = 'ideas_input'
-#set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
-mkdir -p $prep_output_dir &&
-mkdir -p $ideas_input_dir &&
+##set ideas_input_dir = 'ideas_input'
+##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
+##mkdir -p $ideas_input_dir &&
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -126,11 +124,10 @@
     -maxerr $set_max_standard_dev_cond.max_standard_dev
 #end if
 -thread \${GALAXY_SLOTS:-4}
--o $prep_output_dir
-&& mv $prep_output_dir/*cluster $output_cluster
-&& mv $prep_output_dir/*.para $output_para
-&& mv $prep_output_dir/*.profile $output_profile
-&& mv $prep_output_dir/*.state $output_state
+&& mv *.cluster $output_cluster
+&& mv *.para $output_para
+&& mv *.profile $output_profile
+&& mv *.state $output_state
     ]]></command>
     <configfiles>
         <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat: