# HG changeset patch
# User bzonnedda
# Date 1487843306 18000
# Node ID 866f95468b5b5d5bfe10b5a4076aa848becd302f
# Parent  558f04d1364898e3ab8ed1b92026585d8a34038f
Uploaded

diff -r 558f04d13648 -r 866f95468b5b c_rpkm.xml
--- a/c_rpkm.xml	Thu Feb 23 04:25:31 2017 -0500
+++ b/c_rpkm.xml	Thu Feb 23 04:48:26 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;
-	     python \${CONIFER_PATH}/conifer.py rpkm 
+	     python testtoolshed.g2.bx.psu.edu/repos/bzonnedda/conifer2/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;
-	     python \${CONIFER_PATH}/conifer.py rpkm 
+	     python testtoolshed.g2.bx.psu.edu/repos/bzonnedda/conifer2/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
-     python \${CONIFER_PATH}/conifer.py analyze 
+     python testtoolshed.g2.bx.psu.edu/repos/bzonnedda/conifer2/conifer.py analyze 
      --probes $probesFile 
      --rpkm_dir rpkm_dir  
      --output $outputFile