# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410394072 14400
# Node ID 05e63b38b6eeb67bee1920e137a4350aac1dd821
# Parent  8673c6f733d1b4de6a285a7a513fda47f48b284e
removed perl dependency, kept only bioperl dependency

diff -r 8673c6f733d1 -r 05e63b38b6ee LINKYX_identify_X_linked_SNPs.xml
--- a/LINKYX_identify_X_linked_SNPs.xml	Wed Sep 10 13:22:05 2014 -0400
+++ b/LINKYX_identify_X_linked_SNPs.xml	Wed Sep 10 20:07:52 2014 -0400
@@ -4,7 +4,6 @@
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $output1 $output2 $output3 $output4 $output5</command>
diff -r 8673c6f733d1 -r 05e63b38b6ee LINKYX_identify_Y_linked_SNPs.xml
--- a/LINKYX_identify_Y_linked_SNPs.xml	Wed Sep 10 13:22:05 2014 -0400
+++ b/LINKYX_identify_Y_linked_SNPs.xml	Wed Sep 10 20:07:52 2014 -0400
@@ -4,7 +4,6 @@
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command>
diff -r 8673c6f733d1 -r 05e63b38b6ee LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Wed Sep 10 13:22:05 2014 -0400
+++ b/LINKYX_mpileup_wrapper.xml	Wed Sep 10 20:07:52 2014 -0400
@@ -4,7 +4,6 @@
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_mpileup_wrapper.sh $output $input1 $input2</command>
diff -r 8673c6f733d1 -r 05e63b38b6ee LINKYX_reformat_trinity_header.xml
--- a/LINKYX_reformat_trinity_header.xml	Wed Sep 10 13:22:05 2014 -0400
+++ b/LINKYX_reformat_trinity_header.xml	Wed Sep 10 20:07:52 2014 -0400
@@ -4,7 +4,6 @@
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
         <requirement type="package" version="1.6.922">bioperl</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_reformat_trinity_header.sh $output $input1</command>
diff -r 8673c6f733d1 -r 05e63b38b6ee tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 10 13:22:05 2014 -0400
+++ b/tool_dependencies.xml	Wed Sep 10 20:07:52 2014 -0400
@@ -18,15 +18,11 @@
         <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="a1a111b9faa5" 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>