# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410235058 14400
# Node ID 2c693b9dbd568e91080c3996f67c031eeaf818ef
# Parent  bfe4c7bb91d4a941bbb27e2b2b7e3813d16c3cd2
toolshed3

diff -r bfe4c7bb91d4 -r 2c693b9dbd56 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 02 15:46:31 2014 -0400
+++ b/tool_dependencies.xml	Mon Sep 08 23:57:38 2014 -0400
@@ -21,7 +21,7 @@
         <install version="1.0">
             <actions>
                 <action type="setup_perl_environment">
-                    <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="28865aa39fbb" name="package_perl_5_18" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="perl" version="5.18.1" />
                     </repository>
                    <!-- allow downloading and installing an Perl package from cpan.org-->
@@ -30,6 +30,7 @@
                    <package>Bio::DB::Fasta</package>
                    <package>File::Slurp</package>
                    <package>Bio::DB::Sam</package>
+                   <package>PerlIO::gzip</package>
                 </action>
             </actions>
         </install>
@@ -39,27 +40,23 @@
     </package>
 
      <package name="fastq_groomer" version="1.0.4">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="fastq_groomer" owner="devteam" changeset_revision="1298445c852b" />
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="fastq_groomer" owner="devteam" changeset_revision="06c42572d7c0" />
     </package>
 
-     <package name="trinityrnaseq" version="0.0.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="trinityrnaseq" owner="bhaas" changeset_revision="177bb1b443db" />
-    </package>
-
-     <package name="bwa_wrappers" version="1.2.3">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="bwa_wrappers" owner="devteam" changeset_revision="b4427dbb6ced" />
+     <package name="package_trinityrnaseq_2013_08_14" version="2013_08_14">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_trinityrnaseq_2013_08_14" owner="jjohnson" changeset_revision="df23c0ef83a6" />
     </package>
 
-     <package name="sam_to_bam" version="1.1.4">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="8176b2575aa1" />
+     <package name="package_bwa_0_7_7" version="0.7.7">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_bwa_0_7_7" owner="iuc" changeset_revision="f3d4522dd273" />
     </package>
 
-     <package name="samtools_sort" version="1.0.2">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="samtools_sort" owner="iuc" changeset_revision="38ea74bd4054" />
+     <package name="sam_to_bam" version="1.1.3">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="7095d651c95f" />
     </package>
 
-     <package name="picard" version="1.56.0">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="picard" owner="devteam" changeset_revision="ab1f60c26526" />
+     <package name="picard1106" version="1.106">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="picard1106" owner="devteam" changeset_revision="5d881472c379" />
     </package>
     
 </tool_dependency>
\ No newline at end of file