# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1409684972 14400
# Node ID 38fbf97cfce21abfe934f4b6609759d3019d2ccc
# Parent  1955f03f092e1c240cb1e71068e041ac33788339
new dependencies

diff -r 1955f03f092e -r 38fbf97cfce2 README
--- a/README	Tue Sep 02 14:16:04 2014 -0400
+++ b/README	Tue Sep 02 15:09:32 2014 -0400
@@ -1,19 +1,14 @@
 LinkYX
 
-The pipeline can be executed by the following command:
-
-./runLinkYX.sh email@email.com hostname
-
-Please, make sure that all paths in config_devel are set accordingly.
-Otherwise, use online version available from https://perun.metacentrum.cz/perun-registrar-non/?vo=linkYX
+Fully automated pipeline for detection of sex linked genes using RNA-Seq data
+bitbucket.org/biomonika/linkyx
 
-Also, make sure that the input files are copied into the folder named 'input' and follow naming conventions:
-mother_1.fastx, mother_2.fastx
-father_1.fastx, mother_2.fastx
-daughter_1.fastx, daughter_2.fastx
-son_1.fastx, son_2.fastx
+Please install following dependencies from toolshed:
+toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4
+toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1
+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
 
-Instead of fastx, use fastq or fasta format, depending on the type of your
-data. If only single-end reads are used, do not upload the second file.
-
-If you have any questions, please use following email address: michalovova.monika@gmail.com
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+If you have any questions, please use following email address: biomonika@psu.edu
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diff -r 1955f03f092e -r 38fbf97cfce2 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 02 14:16:04 2014 -0400
+++ b/tool_dependencies.xml	Tue Sep 02 15:09:32 2014 -0400
@@ -37,4 +37,29 @@
             Bundle::BioPerl
         </readme>
     </package>
+
+     <package name="fastq_groomer" version="1.0.4">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="fastq_groomer" owner="devteam" changeset_revision="a347750db1d1" />
+    </package>
+
+     <package name="trinityrnaseq" version="0.0.1">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="trinityrnaseq" owner="bhaas" changeset_revision="a347750db1d1" />
+    </package>
+
+     <package name="bwa_wrappers" version="1.2.3">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="bwa_wrapper" owner="devteam" changeset_revision="a347750db1d1" />
+    </package>
+
+     <package name="sam_to_bam" version="1.1.4">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="a347750db1d1" />
+    </package>
+
+     <package name="samtools_sort" version="1.0.2">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="samtools_sort" owner="iuc" changeset_revision="a347750db1d1" />
+    </package>
+
+     <package name="picard" version="1.56.0">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="rgPicardMarkDups" owner="devteam" changeset_revision="a347750db1d1" />
+    </package>
+    
 </tool_dependency>
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