# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1408994895 14400
# Node ID 535f23f7359513872ed6f322b74728d854703387
# Parent  c0eaad1712e0f8bd5019b93bf02c218ac902cafc
d11

diff -r c0eaad1712e0 -r 535f23f73595 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Aug 25 15:19:09 2014 -0400
+++ b/tool_dependencies.xml	Mon Aug 25 15:28:15 2014 -0400
@@ -17,4 +17,30 @@
         </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">
+                        <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>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>
+                </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.
+        </readme>
+    </package>
 </tool_dependency>
\ No newline at end of file