# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1383924077 21600
# Node ID 2620f7984418e9ffa554add8828d0d6ea7745a05
# Parent  03071ff2e5c9781c724671b55c634e392e0c088e
Update to shear version 0.2.5

diff -r 03071ff2e5c9 -r 2620f7984418 shear_assemble.xml
--- a/shear_assemble.xml	Tue Oct 22 09:55:49 2013 -0500
+++ b/shear_assemble.xml	Fri Nov 08 09:21:17 2013 -0600
@@ -1,7 +1,7 @@
-<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.3">
+<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.5">
   <description>create a personal genome from sdi</description>
   <requirements>
-    <requirement type="package" version="0.2.4">shear</requirement>
+    <requirement type="package" version="0.2.5">shear</requirement>
   </requirements>
   <!--
   <version_command></version_command>
diff -r 03071ff2e5c9 -r 2620f7984418 shear_sv.xml
--- a/shear_sv.xml	Tue Oct 22 09:55:49 2013 -0500
+++ b/shear_sv.xml	Fri Nov 08 09:21:17 2013 -0600
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
-<tool id="shear_sv" name="SHEAR-SV" version="0.0.3">
+<tool id="shear_sv" name="SHEAR-SV" version="0.0.5">
   <description>find SVs and estimate the heterogeneity levels from a BAM</description>
   <requirements>
-    <requirement type="package" version="0.2.4">shear</requirement>
+    <requirement type="package" version="0.2.5">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>
-    <requirement type="package" version="latest">kent</requirement>
+    <requirement type="package" version="latest">blat_server</requirement>
     <requirement type="package" version="3">cap3</requirement>
   </requirements>
   <!--
diff -r 03071ff2e5c9 -r 2620f7984418 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 22 09:55:49 2013 -0500
+++ b/tool_dependencies.xml	Fri Nov 08 09:21:17 2013 -0600
@@ -6,8 +6,8 @@
     <package name="bwa" version="0.6.2">
         <repository changeset_revision="8be5fbfc1548" name="package_bwa_0_6_2" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="kent" version="latest">
-        <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="blat_server" version="latest">
+        <repository changeset_revision="455a4bd49c52" name="package_blat_server" 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" />
@@ -17,12 +17,10 @@
           <readme>
 CREST requires: 
   Bioperl package Bio::DB:Sam  
-  blat - requires license for commercial use
-  cap3 - requires license for commercial use
           </readme>
     </package>
-    <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 name="shear" version="0.2.5">
+        <repository changeset_revision="8c3f8debdb51" name="package_shear_0_2_5" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
 </tool_dependency>