# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410495836 14400
# Node ID 0c7f60054ee3ef7471ec92c76bc17afcf6981222
# Parent  ffe50d004cb4064808b83fba72802688f40dd304
toolshed perl, newest commit, two occurencies - based on toolshed bioperl

diff -r ffe50d004cb4 -r 0c7f60054ee3 sort_bam.sh
--- a/sort_bam.sh	Thu Sep 11 22:01:22 2014 -0400
+++ b/sort_bam.sh	Fri Sep 12 00:23:56 2014 -0400
@@ -3,7 +3,8 @@
 bam_file=$2;
 
 hash samtools 2>/dev/null || { echo "I require samtools in path but it's not installed.  Aborting."; exit 1; }
-echo $LINKYX_PATH
-echo $SAMTOOLS
+echo "LINKYX_PATH:" $LINKYX_PATH
+echo "SAMTOOLS:" $SAMTOOLS
+echo "PATH:" $PATH
 samtools sort $bam_file $results 2>log.txt
 
diff -r ffe50d004cb4 -r 0c7f60054ee3 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 11 22:01:22 2014 -0400
+++ b/tool_dependencies.xml	Fri Sep 12 00:23:56 2014 -0400
@@ -18,13 +18,19 @@
         <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
     </package>
 
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="perl" version="5.18.1">
+      <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </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">
+      <install version="1.0">
+          <actions>
+              <action type="setup_perl_environment">
+                  <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                      <package name="perl" version="5.18.1" />
                     </repository>
-                   <!-- allow downloading and installing an Perl package from cpan.org-->
+                    <!-- 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::Fasta</package>
@@ -38,5 +44,4 @@
             Bundle::BioPerl
         </readme>
     </package>
-
 </tool_dependency>
\ No newline at end of file