# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410477431 14400
# Node ID ea52ef8d7f3a67cdf0a8c902a169e1bda64912d0
# Parent  05e63b38b6eeb67bee1920e137a4350aac1dd821
added perl dependency since galaxy A seems working and added samtools sort

diff -r 05e63b38b6ee -r ea52ef8d7f3a LINKYX_mpileup_wrapper.sh
--- a/LINKYX_mpileup_wrapper.sh	Wed Sep 10 20:07:52 2014 -0400
+++ b/LINKYX_mpileup_wrapper.sh	Thu Sep 11 19:17:11 2014 -0400
@@ -5,8 +5,4 @@
 
 sorted_bam=${bam_file}_sorted
 
-#LINKYX_PATH set during toolshed installation
-
 samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results
-
-#samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt
\ No newline at end of file
diff -r 05e63b38b6ee -r ea52ef8d7f3a LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Wed Sep 10 20:07:52 2014 -0400
+++ b/LINKYX_mpileup_wrapper.xml	Thu Sep 11 19:17:11 2014 -0400
@@ -22,7 +22,7 @@
      </tests>
    
      <help>
-   This tool tests if primers are present in gorilla female or on human Y or chimp Y chromosome.
+   Run mpileup with LINKYX-specific parameters
      </help>
    
    </tool>
\ No newline at end of file
diff -r 05e63b38b6ee -r ea52ef8d7f3a README.txt
--- a/README.txt	Wed Sep 10 20:07:52 2014 -0400
+++ b/README.txt	Thu Sep 11 19:17:11 2014 -0400
@@ -1,14 +1,13 @@
 LinkYX
 
 Fully automated pipeline for detection of sex linked genes using RNA-Seq data
-bitbucket.org/biomonika/linkyx
+
+The installation is described on the project wiki page:
+https://bitbucket.org/biomonika/linkyx/wiki/Home
 
-Please install following dependencies from toolshed:
-toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4
-testtoolshed.g2.bx.psu.edu/view/jjohnson/trinityrnaseq/0.0.2
-toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3
-toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4
-toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2
-toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0
+In order to install additional tools used in the workflow, please install following repository suite definition to the Galaxy:
+https://testtoolshed.g2.bx.psu.edu/view/marten/suite_linkyx_bundle_0_1
+
+Code repositary: bitbucket.org/biomonika/linkyx
 
 If you have any questions, please use following email address: biomonika@psu.edu
\ No newline at end of file
diff -r 05e63b38b6ee -r ea52ef8d7f3a sort_bam.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort_bam.sh	Thu Sep 11 19:17:11 2014 -0400
@@ -0,0 +1,6 @@
+#!/bin/bash
+results=$1;
+bam_file=$2;
+
+samtools sort $bam_file $results 2>log.txt
+
diff -r 05e63b38b6ee -r ea52ef8d7f3a sort_bam.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sort_bam.xml	Thu Sep 11 19:17:11 2014 -0400
@@ -0,0 +1,26 @@
+<tool id="sort_bam" name="sort_bam">
+      <description>Sort bam file based on chromosomal coordinates.</description>
+      <requirements>
+        <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="1.6.922">bioperl</requirement>
+      </requirements>
+      <command interpreter="bash">sort_bam.sh $output $input1</command>
+      <inputs>
+        <param format="bam" name="input1" type="data" label="Alignment file"/>
+      </inputs>
+      <outputs>
+        <data format="bam" name="output" />
+      </outputs>
+  
+     <tests>
+       <test>
+       </test>
+     </tests>
+   
+     <help>
+   Sort bam file based on chromosomal coordinates.
+     </help>
+   
+   </tool>
\ No newline at end of file
diff -r 05e63b38b6ee -r ea52ef8d7f3a tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Sep 10 20:07:52 2014 -0400
+++ b/tool_dependencies.xml	Thu Sep 11 19:17:11 2014 -0400
@@ -18,11 +18,16 @@
         <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">
+                    <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>XML::Parser</package>