# HG changeset patch
# User greg
# Date 1503575656 14400
# Node ID 19112fe6e5bd0e600be9a58b1e32bd3f154acef3
# Parent  2321d1e6237dd042509a5763e9ee8948dbb0804e
Uploaded

diff -r 2321d1e6237d -r 19112fe6e5bd ideas.xml
--- a/ideas.xml	Thu Aug 24 07:44:31 2017 -0400
+++ b/ideas.xml	Thu Aug 24 07:54:16 2017 -0400
@@ -10,7 +10,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set tmp_dir = "tmp"
-#set prep_input_config = "prep_input_config.txt"
 #set prep_output_config = "prep_output_config.txt"
 ##############################################
 ## Create the config file and prepare the data
@@ -21,9 +20,9 @@
     #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-    cp '$gen_prep_input_config' $prep_input_config &&
+    cp '$gen_prep_input_config' "prep_input_config.txt" &&
     prepMat
-    $prep_input_config
+    '$gen_prep_input_config'
     #if str($specify_genomic_window) == "yes":
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
@@ -50,7 +49,7 @@
 ## Coerce the prepMat config output to the
 ## format expected by the R matrix builder.
 ##############################################
-&& cut -d' ' $prep_input_config -f1,2 > file1.txt
+&& cut -d' ' '$gen_prep_input_config' -f1,2 > file1.txt
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################