# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410367714 14400
# Node ID 2cbcdfd5d4896cb807a293138f50840b06975470
# Parent  373cd706d44f7bfcc0b73ac70ad0c11f5b377a61
added perl dependencies

diff -r 373cd706d44f -r 2cbcdfd5d489 LINKYX_identify_X_linked_SNPs.xml
--- a/LINKYX_identify_X_linked_SNPs.xml	Wed Sep 10 11:40:09 2014 -0400
+++ b/LINKYX_identify_X_linked_SNPs.xml	Wed Sep 10 12:48:34 2014 -0400
@@ -3,8 +3,9 @@
       <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>
+        <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>
       <inputs>
diff -r 373cd706d44f -r 2cbcdfd5d489 LINKYX_identify_Y_linked_SNPs.xml
--- a/LINKYX_identify_Y_linked_SNPs.xml	Wed Sep 10 11:40:09 2014 -0400
+++ b/LINKYX_identify_Y_linked_SNPs.xml	Wed Sep 10 12:48:34 2014 -0400
@@ -3,8 +3,9 @@
       <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>
+        <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>
       <inputs>
diff -r 373cd706d44f -r 2cbcdfd5d489 LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Wed Sep 10 11:40:09 2014 -0400
+++ b/LINKYX_mpileup_wrapper.xml	Wed Sep 10 12:48:34 2014 -0400
@@ -3,8 +3,9 @@
       <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>
+        <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>
       <inputs>
diff -r 373cd706d44f -r 2cbcdfd5d489 LINKYX_reformat_trinity_header.xml
--- a/LINKYX_reformat_trinity_header.xml	Wed Sep 10 11:40:09 2014 -0400
+++ b/LINKYX_reformat_trinity_header.xml	Wed Sep 10 12:48:34 2014 -0400
@@ -3,8 +3,9 @@
       <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>
+        <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 $input1</command>
       <inputs>
diff -r 373cd706d44f -r 2cbcdfd5d489 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 10 11:40:09 2014 -0400
+++ b/tool_dependencies.xml	Wed Sep 10 12:48:34 2014 -0400
@@ -2,6 +2,22 @@
     <set_environment version="1.0">
         <environment_variable name="LINKYX_PATH" action="set_to">$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>
+
     <package name="perl" version="5.18.1">
         <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" />
     </package>
@@ -9,16 +25,16 @@
         <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 changeset_revision="091a97f8c585" 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>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>
-                   <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>
+                   <package>Bio::DB::Sam</package>
+                   <package>PerlIO::gzip</package>
                 </action>
             </actions>
         </install>
@@ -26,4 +42,5 @@
             Bundle::BioPerl
         </readme>
     </package>
+
 </tool_dependency>
\ No newline at end of file