Mercurial > repos > biomonika > linkyx

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edited README file
author biomonika <biomonika@psu.edu>
date Fri, 20 Feb 2015 14:50:31 -0500
parents 8fbe25248354
children 939e59027486
files README.txt
diffstat 1 files changed, 32 insertions(+), 7 deletions(-) [+]
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--- a/README.txt	Tue Feb 17 22:57:24 2015 -0500
+++ b/README.txt	Fri Feb 20 14:50:31 2015 -0500
@@ -1,13 +1,38 @@
-LinkYX
+**Fully automated pipeline for detection of sex linked genes using RNA-Seq data**
+
+This pipeline has been designed for detection of sex-linked genes from the cross using RNASeq data. It contains two workflows, one for detection of Y-linked and one for detection of X-linked genes.
 
-Fully automated pipeline for detection of sex linked genes using RNA-Seq data
+INSTALLING PREREQUISITES
+You will need 3 prerequisites in order to successfully run this pipeline:
+1) install linkyx
+2) install tool dependencies
+3) import workflows
 
-The installation is described on the project wiki page:
-https://bitbucket.org/biomonika/linkyx/wiki/Home
+1) The easiest way how to install linkyx tools is to login to your local Galaxy instance and click Admin -> Search and browse tool sheds -> Galaxy tool shed -> linkyx
+
+Click on the tool and then simply press button "Install to Galaxy" in the upper part of the screen.
+This tool repository contains four tools:
+LINKYX_X
+Identify X linked contigs from cross
 
-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
+LINKYX_Y
+Identify Y linked contigs from cross
+
+LINKYX_mpileup
+Run mpileup with LINKYX-specific parameters
+
+Reformat Trinity header
+
+All tools can be run independently, but the easiest way to obtain proper input files is via provided workflows.
 
-Code repositary: bitbucket.org/biomonika/linkyx
+2) The dependencies can be installed in a similar fashion as linkyx tool from the Galaxy tool shed by searching for suite_linkyx_1_0
+
+3) When installing linkyx from toolshed, you can click on the "Workflows" on the main page describing the tool in the section "Contents of this repository". After clicking on either linkY or linkX, you will be presented an option to install the workflows by clicking "Install to Galaxy" button
 
+RUNNING THE WORKFLOWS
+After you imported workflows to the galaxy and installed linkyx and workflow dependencies, the pipeline is ready to go. 
+
+You can access it by clicking on the "Workflow" in the upper gray layer of your Galaxy instance. After clicking on the name of the workflow and choosing "Run", you will be requested to select input datasets, two for each member of the cross since paired-end reads are expected by default. If you don't have your data yet, test files are available in this repository. The computation for these files ends in ~5 minutes and outputs one X-linked and one Y-linked contig.
+
+CONTACT INFORMATION
 If you have any questions, please use following email address: biomonika@psu.edu
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