# HG changeset patch
# User stef
# Date 1412937238 14400
# Node ID 3419fc80819330722f172eec37792d56b8a8301e
# Parent  02e5aee670dea0c9b4b060e5196a2b607c0f324c
Uploaded

diff -r 02e5aee670de -r 3419fc808193 falco-call.xml
--- a/falco-call.xml	Fri Oct 10 06:28:46 2014 -0400
+++ b/falco-call.xml	Fri Oct 10 06:33:58 2014 -0400
@@ -3,12 +3,12 @@
   <requirements>
     
     <requirement type="package" version="0.1.19">samtools</requirement>
-
     <requirement type="package" version="3.1.0">R</requirement>
+    <requirement type="package" version="2">bcftools</requirement> 
     <!--
     <requirement type="package" version="3.4">snpeff</requirement>
     <requirement type="package" version="2">varscan</requirement> 
-    <requirement type="package" version="2">bcftools</requirement> 
+    
     -->
     <!--
     
diff -r 02e5aee670de -r 3419fc808193 falco/init.sh
--- a/falco/init.sh	Fri Oct 10 06:28:46 2014 -0400
+++ b/falco/init.sh	Fri Oct 10 06:33:58 2014 -0400
@@ -24,13 +24,15 @@
 #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
 
 #varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
-java=/usr/bin/java
+#java=/usr/bin/java
 #bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa
 #flash=/ccagc/lib/flash/FLASH-1.2.2/flash
 
diff -r 02e5aee670de -r 3419fc808193 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Oct 10 06:28:46 2014 -0400
+++ b/tool_dependencies.xml	Fri Oct 10 06:33:58 2014 -0400
@@ -10,12 +10,13 @@
         <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
-    <!--
+    
     <package name="bcftools" version="2">
-        <repository name="bcftools" owner="iuc" prior_installation_required="TRUE" />
+        <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
         <readme>Let's see where this msg appears...bcftools</readme>
     </package>
     
+    <!--
     <package name="snpeff" version="3.4">
         <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" />
         <readme>Let's see where this msg appears...snpeff</readme>