--- a/ideas.xml	Thu Aug 10 12:41:43 2017 -0400
+++ b/ideas.xml	Thu Aug 10 12:46:17 2017 -0400
@@ -9,7 +9,8 @@
     </requirements>
     <command><![CDATA[
 #import os
-mkdir -p tmp &&
+#set tmp_dir = ($os.path.join($os.getcwd(), 'tmp')
+mkdir -p $tmp_dir &&
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -53,16 +54,16 @@
 ## Build the R matrix from the prepMat output
 ##############################################
 #set r_matrix_input = None
-#for f in $os.listdir('tmp'):
+#for f in $os.listdir($tmp_dir):
     #if f.endswith('.bed.gz'):
-        #set r_matrix_input = $os.path.join('tmp', f)
+        #set r_matrix_input = $os.path.join($tmp_dir, $f)
     #end if
 #end for
 #assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty."
 && Rscript '$__tool_directory__/build_matrix.R'
 -i $r_matrix_input
 -o '%s.input' % $f
--w 'tmp'
+-w $tmp_dir
 ##############################################
 ## Run IDEAS on the R matrix
 ##############################################