# HG changeset patch
# User stef
# Date 1412949026 14400
# Node ID 12f7ce7de71f8799f5f3b15d89717dc14114c55a
# Parent  3d3afdb4a34f18b3dfe496dbc2632cd51ecc15ee
Uploaded

diff -r 3d3afdb4a34f -r 12f7ce7de71f falco-call.sh
--- a/falco-call.sh	Fri Oct 10 08:56:00 2014 -0400
+++ b/falco-call.sh	Fri Oct 10 09:50:26 2014 -0400
@@ -44,6 +44,8 @@
 #echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file
 #echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file
 #echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file
+echo "samtools=samtools" >> $init_file
+echo "bcftools=bcftools" >> $init_file
 
 ## files
 echo "targetBed=$BED_PATH" >> $init_file
diff -r 3d3afdb4a34f -r 12f7ce7de71f falco/init.sh
--- a/falco/init.sh	Fri Oct 10 08:56:00 2014 -0400
+++ b/falco/init.sh	Fri Oct 10 09:50:26 2014 -0400
@@ -24,9 +24,7 @@
 #qTrim=/ccagc/bin/fastq_quality_trimmer
 #stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py
 #samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools
-samtools=samtools
 #bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools
-bcftools=bcftools
 #snpEff=/ccagc/lib/snpEff/snpEff_3_0a
 #snpEff=/ccagc/lib/snpEff/snpEff_v3_4
 #snpSift=/ccagc/lib/SnpSift