# HG changeset patch
# User stef
# Date 1410446992 14400
# Node ID c84ed1b12d67250123c231f397e5ee3cd72ad53e
# Parent  cebbd6a924119b5105a23147282f7db4f454b756
Uploaded

diff -r cebbd6a92411 -r c84ed1b12d67 falco.sh
--- a/falco.sh	Thu Sep 11 06:59:12 2014 -0400
+++ b/falco.sh	Thu Sep 11 10:49:52 2014 -0400
@@ -64,11 +64,20 @@
 echo "HTMLOUT: "$html_out
 echo "VCFOUT : "$vcf_out
 echo "INIT   : "$init_file
+
 source $init_file
+
 echo "--- sam ---"
 samtools
 echo "--- bcf ---"
 bcftools
+echo "--- snpsift ---"
+java -jar $snpSift/SnpSift.jar
+echo "--- snpeff ---"
+java -jar $snpEff/snpeff.jar
+echo "--- varscan ---"
+java -jar $varScan
+
 exit 0
 
 ## ----------
diff -r cebbd6a92411 -r c84ed1b12d67 falco.xml
--- a/falco.xml	Thu Sep 11 06:59:12 2014 -0400
+++ b/falco.xml	Thu Sep 11 10:49:52 2014 -0400
@@ -9,6 +9,8 @@
     <requirement type="package" version="2">bcftools</requirement> 
     <!--
     -->
+    <requirement type="set_environment">JAVA_JAR_PATH</requirement>
+    <requirement type="set_environment">SNPEFF_JAR_PATH</requirement>
     <requirement type="set_environment">TOOL_DIR</requirement>
   </requirements>
 
diff -r cebbd6a92411 -r c84ed1b12d67 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 11 06:59:12 2014 -0400
+++ b/tool_dependencies.xml	Thu Sep 11 10:49:52 2014 -0400
@@ -33,4 +33,6 @@
         <readme>Let's see where this msg appears...ENV VAR</readme>
     </set_environment>
     
+    <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>-->
+    
 </tool_dependency>