# HG changeset patch
# User stef
# Date 1410433018 14400
# Node ID 90badfe82b95a11a1ddd4c7cb6752d992bcf2d25
# Parent  f34be89e96749545afd73851f1541aa17050ce66
Uploaded

diff -r f34be89e9674 -r 90badfe82b95 README.rst
--- a/README.rst	Thu Sep 11 06:40:27 2014 -0400
+++ b/README.rst	Thu Sep 11 06:56:58 2014 -0400
@@ -14,15 +14,6 @@
 July 2014        * first release in Test Tool Shed
 ============== ========================================================================
 
-Tool Versioning
-===============
-
-Tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.
-
 
 Bug Reports & other questions
 =============================
diff -r f34be89e9674 -r 90badfe82b95 falco.sh
--- a/falco.sh	Thu Sep 11 06:40:27 2014 -0400
+++ b/falco.sh	Thu Sep 11 06:56:58 2014 -0400
@@ -64,6 +64,12 @@
 echo "HTMLOUT: "$html_out
 echo "VCFOUT : "$vcf_out
 echo "INIT   : "$init_file
+source $init_file
+echo "--- sam ---"
+samtools
+echo "--- bcf ---"
+bcftools
+exit 0
 
 ## ----------
 ## create output files dir
diff -r f34be89e9674 -r 90badfe82b95 falco/init.sh
--- a/falco/init.sh	Thu Sep 11 06:40:27 2014 -0400
+++ b/falco/init.sh	Thu Sep 11 06:56:58 2014 -0400
@@ -23,13 +23,13 @@
 adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt
 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
-bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools
+#samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools
+#bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools
 #snpEff=/ccagc/lib/snpEff/snpEff_3_0a
-snpEff=/ccagc/lib/snpEff/snpEff_v3_4
-snpSift=/ccagc/lib/SnpSift
+#snpEff=/ccagc/lib/snpEff/snpEff_v3_4
+#snpSift=/ccagc/lib/SnpSift
 
-varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
+#varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar
 java=/usr/bin/java
 bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa
 flash=/ccagc/lib/flash/FLASH-1.2.2/flash
@@ -53,5 +53,5 @@
 errorRate=$DIR/misc/errorRate.pl
 plotQc=$DIR/misc/plotsQC.R
 
-export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/
+#export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/
 source ./galaxy_init.sh
diff -r f34be89e9674 -r 90badfe82b95 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 11 06:40:27 2014 -0400
+++ b/tool_dependencies.xml	Thu Sep 11 06:56:58 2014 -0400
@@ -7,8 +7,8 @@
         <readme>Let's see where this msg appears...R</readme>
     </package>
     
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" />
         <readme>Let's see where this msg appears...samtools</readme>
     </package>
 
diff -r f34be89e9674 -r 90badfe82b95 tool_dependencies_MAINTOOLSHED.xml
--- a/tool_dependencies_MAINTOOLSHED.xml	Thu Sep 11 06:40:27 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    
-    <package name="R" version="3.0.3">
-        <repository name="package_r_3_0_3" toolshed="http://toolshed.g2.bx.psu.edu" owner="iuc" changeset_revision="f386d7431fe0" />
-        <readme>Let's see where this msg appears...R</readme>
-    </package>
-    
-    <package name="samtools" version="0.1.18">
-        <repository name="package_samtools_0_1_18" toolshed="http://toolshed.g2.bx.psu.edu" owner="devteam" changeset_revision="171cd8bc208d"/>
-        <readme>Let's see where this msg appears...samtools</readme>
-    </package>
-    
-    <package name="snpeff" version="3.4">
-        <repository name="package_snpeff_3_4" toolshed="http://toolshed.g2.bx.psu.edu" owner="iuc" changeset_revision="af7ff8187d09"/>
-        <readme>Let's see where this msg appears...snpeff</readme>
-    </package>
-    
-    <package name="varscan" version="2">
-        <repository name="varscan_version_2" toolshed="http://toolshed.g2.bx.psu.edu" owner="devteam" changeset_revision="6f8cead3dc93"/>
-        <readme>Let's see where this msg appears...varscan</readme>
-    </package>
-    
-    <!-- TXT -->
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable>
-        <readme>Let's see where this msg appears...ENV VAR</readme>
-    </set_environment>
-    
-</tool_dependency>