# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1382448052 18000
# Node ID 8180f6b0249b458b5a4bb891a0f8473b559013c2
# Parent  0158f7356ffd915178d287f05d2a15c3b84088e2
Upgrade to SHEAR version 0.2.4

diff -r 0158f7356ffd -r 8180f6b0249b shear_assemble.xml
--- a/shear_assemble.xml	Mon Oct 21 08:54:58 2013 -0500
+++ b/shear_assemble.xml	Tue Oct 22 08:20:52 2013 -0500
@@ -1,7 +1,7 @@
-<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.2">
+<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.3">
   <description>create a personal genome from sdi</description>
   <requirements>
-    <requirement type="package" version="0.2.3">shear</requirement>
+    <requirement type="package" version="0.2.4">shear</requirement>
   </requirements>
   <!--
   <version_command></version_command>
diff -r 0158f7356ffd -r 8180f6b0249b shear_sv.xml
--- a/shear_sv.xml	Mon Oct 21 08:54:58 2013 -0500
+++ b/shear_sv.xml	Tue Oct 22 08:20:52 2013 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="shear_sv" name="SHEAR-SV" version="0.0.2">
+<tool id="shear_sv" name="SHEAR-SV" version="0.0.3">
   <description>find SVs and estimate the heterogeneity levels from a BAM</description>
   <requirements>
-    <requirement type="package" version="0.2.3">shear</requirement>
+    <requirement type="package" version="0.2.4">shear</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="package" version="0.6.2">bwa</requirement>
     <requirement type="package" version="1.0.1">crest</requirement>
diff -r 0158f7356ffd -r 8180f6b0249b tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Oct 21 08:54:58 2013 -0500
+++ b/tool_dependencies.xml	Tue Oct 22 08:20:52 2013 -0500
@@ -9,16 +9,20 @@
     <package name="kent" version="latest">
         <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="cap3" version="3">
+        <repository changeset_revision="a472ccd208e2" name="package_cap3_3" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="crest" version="1.0.1">
         <repository changeset_revision="89a9d6ce7f96" name="package_crest_1_0_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
           <readme>
 CREST requires: 
   Bioperl package Bio::DB:Sam  
-  cap3 which only has binary executable downloads from:   http://seq.cs.iastate.edu/cap3.html
+  blat - requires license for commercial use
+  cap3 - requires license for commercial use
           </readme>
     </package>
-    <package name="shear" version="0.2.3">
-        <repository changeset_revision="8bcf811b9c1e" name="package_shear_0_2_3" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="shear" version="0.2.4">
+        <repository changeset_revision="d6a7b8497a7b" name="package_shear_0_2_4" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
 </tool_dependency>