# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1408985490 14400
# Node ID 5573c2fa98241ceb9b9d504af4de6ca31b75a48e
# Parent  2e1f6f189689482c73a10342fdb6efbfd3aed393
full depend

diff -r 2e1f6f189689 -r 5573c2fa9824 test_dependency.sh
--- a/test_dependency.sh	Sun Aug 24 22:56:50 2014 -0400
+++ b/test_dependency.sh	Mon Aug 25 12:51:30 2014 -0400
@@ -2,14 +2,12 @@
 
 results=$1 #X-linked candidates written here
 
-fake_input1=${2}
-fake_input2=${3}
-
 echo "LINKYX_PATH: " $LINKYX_PATH
+echo "SAMTOOLS: " $SAMTOOLS
 
 perl ${LINKYX_PATH}/test.pl
 
-#cat ${LINKYX_PATH}/demo_files/reference.fasta >>$results
+echo "LINKYX_PATH: " $LINKYX_PATH "SAMTOOLS: " $SAMTOOLS >>$results
 
 
 
diff -r 2e1f6f189689 -r 5573c2fa9824 test_dependency.xml
--- a/test_dependency.xml	Sun Aug 24 22:56:50 2014 -0400
+++ b/test_dependency.xml	Mon Aug 25 12:51:30 2014 -0400
@@ -1,12 +1,10 @@
 <tool id="test_dependency" name="test_dependency">
       <description>Test toolshed dependency</description>
-      <command interpreter="bash">test_dependency.sh $output $input1 $input2</command>
+      <command interpreter="bash">test_dependency.sh $output</command>
       <inputs>
-        <param format="fastq" name="input1" type="data" label="Fake left reads"/>
-        <param format="fastq" name="input2" type="data" label="Fake right reads"/>
       </inputs>
       <outputs>
-        <data format="fasta" name="output" />
+        <data format="txt" name="output" />
       </outputs>
   
      <tests>
diff -r 2e1f6f189689 -r 5573c2fa9824 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Aug 24 22:56:50 2014 -0400
+++ b/tool_dependencies.xml	Mon Aug 25 12:51:30 2014 -0400
@@ -2,4 +2,44 @@
     <set_environment version="1.0">
         <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
+    <package name="samtools_fPIC" version="1.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
+                <action type="shell_command">sed -i 's/O2/O2 -fPIC/‘ Makefile </action>
+                <action type="shell_command">make </action>
+                <action type="make_directory">$INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR/bin</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>
+    
+    <package name="bioperl" version="1.6.922">
+        <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>
+                   <!-- 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>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>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installing dependencies. Bio::DB::Sam needs to know location of bam.h and compiled libbam.a files, therefore environmental variable SAMTOOLS needs to be correctly set.
+        </readme>
+    </package>
 </tool_dependency>