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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.