MGEScan on Galaxy Scientific Workflow

A Galaxy based system for identifying retrotransposons in genome

• Tutorial
• Documentation
• Source
• Home Page

Prerequisite

Python

• git
• virtualenv
• python-dev

sudo apt-get update
sudo apt-get install python-virtualenv -y
sudo apt-get install git -y
sudo apt-get install python-dev -y

Virtualenv

mkdir ~/virtualenv
virtualenv ~/virtualenv/mgescan
source ~/virtualenv/mgescan/bin/activate
echo "source ~/virtualenv/mgescan/bin/activate" >> ~/.bash_profile

Tools

• Galaxy
• HMMER
• EMBOSS
• trf (Tandem Repeats Finder)

Galaxy

cd ~/
git clone https://github.com/galaxyproject/galaxy/

HMMER and EMBOSS

Ubuntu

sudo apt-get install hmmer -y
sudo apt-get install emboss -y

trf

wget http://tandem.bu.edu/trf/downloads/trf407b.linux64
mv trf407b.linux64 ~/virtualenv/mgescan/bin/trf
chmod 700 ~/virtualenv/mgescan/bin/trf

RepeatMasker

cd ~
wget http://www.repeatmasker.org/RepeatMasker-open-4-0-5.tar.gz
tar xvzf RepeatMasker-open-4-0-5.tar.gz

Find the latest at: http://www.repeatmasker.org/RMDownload.html

Installation

git clone https://github.com/MGEScan/mgescan.git
cd mgescan
python setup.py install

virtualenv (optional for individual without sudo)

virtualenv ~/virtualenv/mgescan
source ~/virtualenv/mgescan/bin/activate

Galaxy modification

cd ~/
cp -pr ~/mgescan/galaxy-modified/* ~/galaxy

Start Galaxy

cd ~/galaxy
./run.sh &

Default port number : 38080 http://[IP ADDRESS]:38080

Command Line Tool (mgescan)

Usage:
    mgescan both <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan ltr <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan nonltr <genome_dir> [--output=<data_dir>] [--mpi=<num>]
    mgescan (-h | --help)
    mgescan --version

Amazon Cloud Image (EC2)

• US East (Ohio) Region Only
• MGEScan - ami-394ebd52 (latest version)
• retrotminer-alpha - ami-23d9c74a (created at 2014)

Old AMIs need to get an update of MGEScan, run the following commands after launching a new instance, and restart the server.

(Stop galaxy server first - processs looks like 'python ./scripts/paster.py serve universe_wsgi.ini')
sudo yum update -y
cd $MGESCAN_SRC;git pull;python setup.py install
cd $GALAXY_HOME;git pull;./run.sh;sh manage_db.sh -c ./universe_wsgi.ini upgrade
cp -pr $MGESCAN_SRC/galaxy-modified/* $GALAXY_HOME
cd $GALAXY_HOME;nohup bash run.sh &

Citation

@article{lee2016mgescan, title={MGEScan: a Galaxy-based system for identifying retrotransposons in genomes}, author={Lee, Hyungro and Lee, Minsu and Mohammed Ismail, Wazim and Rho, Mina and Fox, Geoffrey C and Oh, Sangyoon and Tang, Haixu}, journal={Bioinformatics}, volume={32}, number={16}, pages={2502--2504}, year={2016}, publisher={Oxford University Press} }

Web Sites

• MGEScan-LTR
• MGEScan-nonLTR

License

Copyright (C) 2015. See the LICENSE file for license rights and limitations (GPL v3).

This program is part of MGEScan.

MGEScan is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.