# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410363609 14400
# Node ID 373cd706d44f7bfcc0b73ac70ad0c11f5b377a61
# Parent  a4f2492ce714a704789c863fc73b4a1cfbb0db71
toolshed15

diff -r a4f2492ce714 -r 373cd706d44f tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 10 11:30:31 2014 -0400
+++ b/tool_dependencies.xml	Wed Sep 10 11:40:09 2014 -0400
@@ -2,34 +2,23 @@
     <set_environment version="1.0">
         <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
-
-    <package name="samtools" version="0.1.19">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
-                <action type="shell_command">sed -i 's/O2/O2 -fPIC/' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
+    <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="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://testtoolshed.g2.bx.psu.edu">
                         <package name="perl" version="5.18.1" />
                     </repository>
                    <!-- allow downloading and installing an Perl package from cpan.org-->
-                   <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::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>Bio::DB::Sam</package>
+                   <package>http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/File-Slurp-9999.13.tar.gz</package>
                 </action>
             </actions>
         </install>