TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets.
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genomes
run
test-data
LICENSE.txt
README
TargetOrtho.xml
respository_dependencies.xml
tool_dependencies.xml

README

Use TargetOrtho now at: http://ec2-23-20-137-161.compute-1.amazonaws.com/
Reference: 
   Lori Glenwinkel, Di Wu, Gregory Minevich and Oliver Hobert. TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets. Genetics May 1, 2014 vol. 197 no. 1 61-76. http://hobertlab.org/wp-content/uploads/2014/11/TargetOrtho.pdf

System Requirements:
   x86_64 GNU/Linux
   MEME package version 4.9.1 
   python 2.7+
   python modules:
      scipy
      numpy
      matplotlib

Tested on Amazon EC2 instance using ubuntu-precise-12.04-amd64-server-20131003

To run TargetOrtho on your own Amazon EC2 instance:
   1. find our AMI with TargetOrtho dependencies installed in Amazon Community AMIs*: GalaxyTargetOrtho1.1 (ami-0076e068)
   2. See below for INSTALL instructions
   Note: *TargetOrtho AMI is only available from Amazon's "US East" region community AMIs. T0 copy an AMI to your region see: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/CopyingAMIs.html

INSTALL 
git clone https://github.com/loriglenwinkel/TargetOrtho.git 
OR download directly using "Download Zip" button at https://github.com/loriglenwinkel/TargetOrtho

Before running TargetOrtho for the first time, unpack the following compressed files from the command line:
   1. Navigate into the TargetOrtho/run directory:
   tar -zxvf TargetOrtho.db.tar.gz
   
   2. Navigate into the run/genomes/ directory. For each genome in the genomes folder: 
   
   tar -zxvf *.tar.gz
   
   note:* =each filename.tar.gz. For example: c_eleg_WS220.tar.gz. User must have full priveleges to execute each command.
   3. Navidate to the run directory. Give permissions to each directory within using the command: sudo chmod ugo+wrx ./*

To add TargetOrtho as a galaxy tool in a local galaxy instance manually:
   1. Install galaxy instance: See http://wiki.galaxyproject.org/Admin/Get%20Galaxy
   2. Place the uncompressed TargetOrtho directory in the tools directory found in the galaxy root directory. (path_to_galaxy/tools/TargetOrtho) 
   3. Add the following line to the tool_conf.xml in the desired secion of the toolbox (tool_conf.xml is found in the galaxy root directory:path_to_galaxy/tool_conf.xml)
       <tool file="TargetOrtho/TargetOrtho.xml"/>
   4. Restart galaxy

To run TargetOrtho from the command line:
   navigatel to TargetOrtho/run/scripts
   command: python TargetOrtho.py -h
   Description: shows TargetOrtho usage including default parameters.
   Note: user must have full privildges to execute scripts (may need run with sudo before command).
   
To run TargetOrtho with example files:
   Example 1: 1 motif
   navigate to TargetOrtho/run/scripts
   command: python TargetOrtho.py -f ../examples/meme_1motif.txt -q ../examples/query_genes.txt -w True 
   Description: runs TargetOrtho using a meme formatted input file and a query list of genes. The query only option is set to True (-w True) so that only query gene results are reported (opposed to whole genome results plus query gene results). Results are output to TargetOrtho/output/ by default.
   
   Example 2: CRM (2 motif search)
   navigate to TargetOrtho/run/scripts
   command: python TargetOrtho.py -f ../examples/meme_2motifs.txt -q ../examples/query_genes.txt -w True -P '1e-4 1e-5'
   Description: runs TargetOrtho using a meme formatted input file conatining two motifs and using a query list of genes. The query only option is set to True (-w True) so that only query gene results are reported (opposed to whole genome results plus query gene results). Resulting candidate genes have a least one of each input motif (see CRM results files). Results are output to TargetOrtho/output/ by default.