# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410360596 14400
# Node ID ef5c8ed727b046175b3c3436945dc1588dc7f606
# Parent  36feb5af775a27d20072916ad74790876da59e37
toolshed12

diff -r 36feb5af775a -r ef5c8ed727b0 LINKYX_identify_X_linked_SNPs.xml
--- a/LINKYX_identify_X_linked_SNPs.xml	Wed Sep 10 10:42:57 2014 -0400
+++ b/LINKYX_identify_X_linked_SNPs.xml	Wed Sep 10 10:49:56 2014 -0400
@@ -3,6 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
+        <requirement type="set_environment">PERL_PATH</requirement>
         <requirement type="package" version="0.1.19">samtools</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 36feb5af775a -r ef5c8ed727b0 LINKYX_identify_Y_linked_SNPs.xml
--- a/LINKYX_identify_Y_linked_SNPs.xml	Wed Sep 10 10:42:57 2014 -0400
+++ b/LINKYX_identify_Y_linked_SNPs.xml	Wed Sep 10 10:49:56 2014 -0400
@@ -3,6 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
+        <requirement type="set_environment">PERL_PATH</requirement>
         <requirement type="package" version="0.1.19">samtools</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 36feb5af775a -r ef5c8ed727b0 LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Wed Sep 10 10:42:57 2014 -0400
+++ b/LINKYX_mpileup_wrapper.xml	Wed Sep 10 10:49:56 2014 -0400
@@ -3,6 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
+        <requirement type="set_environment">PERL_PATH</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_mpileup_wrapper.sh $output $input1 $input2</command>
diff -r 36feb5af775a -r ef5c8ed727b0 LINKYX_reformat_trinity_header.xml
--- a/LINKYX_reformat_trinity_header.xml	Wed Sep 10 10:42:57 2014 -0400
+++ b/LINKYX_reformat_trinity_header.xml	Wed Sep 10 10:49:56 2014 -0400
@@ -3,6 +3,7 @@
       <requirements>
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
+        <requirement type="set_environment">PERL_PATH</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_reformat_trinity_header.sh $output $input1</command>
diff -r 36feb5af775a -r ef5c8ed727b0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 10 10:42:57 2014 -0400
+++ b/tool_dependencies.xml	Wed Sep 10 10:49:56 2014 -0400
@@ -32,10 +32,10 @@
                    <package>Bio::DB::Sam</package>
                    <package>PerlIO::gzip</package>
                 </action>
-                <action type="shell_command">export PERL5LIB=$INSTALL_DIR</action>
                 <action type="set_environment">
                     <environment_variable name="PERL_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>
+                <action type="shell_command">export PERL5LIB=$INSTALL_DIR</action>
             </actions>
         </install>
         <readme>