# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1408995753 14400
# Node ID 479f6826477baf47bccaadd7c5265ac5ebfe2d48
# Parent  535f23f7359513872ed6f322b74728d854703387
d12

diff -r 535f23f73595 -r 479f6826477b tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 25 15:28:15 2014 -0400
+++ b/tool_dependencies.xml	Mon Aug 25 15:42:33 2014 -0400
@@ -17,30 +17,27 @@
         </install>
         <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
     </package>
-
     <package name="perl" version="5.18.1">
         <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
     </package>
-    
     <package name="bioperl" version="1.6.922">
         <install version="1.0">
             <actions>
                 <action type="setup_perl_environment">
-                    <repository changeset_revision="28865aa39fbb" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="perl" version="5.18.1" />
                     </repository>
                    <!-- allow downloading and installing an Perl package from cpan.org-->
-                   <package>Bio::DB::Sam</package>
-                   <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package>
+                   <package>XML::Parser</package>
+                   <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
                    <package>Bio::DB::Fasta</package>
-                   <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package>
                    <package>File::Slurp</package>
-                   <package>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package>
+                   <package>Bio::DB::Sam</package>
                 </action>
             </actions>
         </install>
         <readme>
-            Installing dependencies. Bio::DB::Sam needs to know location of bam.h and compiled libbam.a files, therefore environmental variable SAMTOOLS needs to be correctly set.
+            Bundle::BioPerl
         </readme>
     </package>
 </tool_dependency>
\ No newline at end of file