# HG changeset patch
# User bzonnedda
# Date 1487845831 18000
# Node ID c56e89c84654ed1ec836ab5336c9ca74ff26132b
# Parent  6c2b538f2cc6c63fb50255980384525363aca7d3
Uploaded

diff -r 6c2b538f2cc6 -r c56e89c84654 c_rpkm.xml
--- a/c_rpkm.xml	Thu Feb 23 05:22:05 2017 -0500
+++ b/c_rpkm.xml	Thu Feb 23 05:30:31 2017 -0500
@@ -6,20 +6,20 @@
 	#if str($input_bam.label.value) != "":
 	     ln -s ${input_bam.inputFile} ${$input_bam.label.value}.bam;
 	     ln -s ${input_bam.inputFile.metadata.bam_index} ${$input_bam.label.value}.bam.bai;
-	     conifer.py rpkm 
+	     python \${CONIFER_PATH}/conifer.py rpkm 
 	     --probes $probesFile 
 	     --input ${$input_bam.label.value}.bam
 	     --output rpkm_dir/${$input_bam.label.value}.txt;
 	#else
 	     ln -s ${input_bam.inputFile} ${input_bam.inputFile.dataset.name}.bam;
 	     ln -s ${input_bam.inputFile.metadata.bam_index} ${input_bam.inputFile.dataset.name}.bam.bai;
-	     conifer.py rpkm 
+	     python \${CONIFER_PATH}/conifer.py rpkm 
 	     --probes $probesFile 
 	     --input ${input_bam.inputFile.dataset.name}.bam
 	     --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt;
 	#end if
 #end for
-     conifer.py analyze 
+     python \${CONIFER_PATH}/conifer.py analyze 
      --probes $probesFile 
      --rpkm_dir rpkm_dir  
      --output $outputFile