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docs/source/aws.rst (5344, 2018-05-15)
docs/source/blockdiag.rst (1954, 2018-05-15)
docs/source/conf.py (8152, 2018-05-15)
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docs/source/images/EC-10.JPG (177275, 2018-05-15)
docs/source/images/EC-11.JPG (85989, 2018-05-15)
docs/source/images/EC-3.JPG (107905, 2018-05-15)
docs/source/images/EC-5.JPG (142529, 2018-05-15)
docs/source/images/EC-9.JPG (164074, 2018-05-15)
docs/source/images/aws-finding-image.png (79083, 2018-05-15)
docs/source/images/aws-management-console.png (411578, 2018-05-15)
docs/source/images/aws-signin.png (228961, 2018-05-15)
docs/source/images/galaxy-create-a-symlink.png (53476, 2018-05-15)
docs/source/images/galaxy-download.png (19279, 2018-05-15)
docs/source/images/galaxy-importing-from-dataset.png (34163, 2018-05-15)
docs/source/images/galaxy-importing-from-dataset2.png (63239, 2018-05-15)
docs/source/images/galaxy-login.png (20395, 2018-05-15)
docs/source/images/galaxy-register.png (49367, 2018-05-15)
docs/source/images/galaxy-run-mgescan.png (105283, 2018-05-15)
docs/source/images/galaxy-view-data.png (17105, 2018-05-15)
docs/source/images/mgescan-description.png (260493, 2018-05-15)
docs/source/images/mgescan-genome-browser.png (39335, 2018-05-15)
docs/source/images/mgescan-ltr-gff3-ensembl.png (344812, 2018-05-15)
docs/source/images/mgescan-ltr-gff3-ucsc-browser.png (331524, 2018-05-15)
docs/source/images/mgescan-ltr.png (207540, 2018-05-15)
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docs/source/images/mgescan-nonltr.png (143982, 2018-05-15)
docs/source/images/mgescan-private-workflow.png (91723, 2018-05-15)
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docs/source/images/mgescan-result.png (46314, 2018-05-15)
docs/source/images/mgescan-test-results.png (22665, 2018-05-15)
docs/source/images/mgescan-tool.png (36224, 2018-05-15)
docs/source/images/mgescan-workflow-both.png (108455, 2018-05-15)
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MGEScan on Galaxy Scientific Workflow =============================================================================== A Galaxy based system for identifying retrotransposons in genome  * [Tutorial](http://mgescan.readthedocs.org/en/latest/tutorial.html) * [Documentation](http://mgescan.readthedocs.org/en/latest/index.html) * [Source](https://github.com/MGEScan/mgescan/) * [Home Page](http://mgescan.github.io/mgescan/) Prerequisite ------------------------------------------------------------------------------- ### Python * git * virtualenv * python-dev ```sh 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 ```sh 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 ```sh cd ~/ git clone https://github.com/galaxyproject/galaxy/ ``` #### HMMER and EMBOSS *Ubuntu* ```sh sudo apt-get install hmmer -y sudo apt-get install emboss -y ``` #### trf ```sh wget http://tandem.bu.edu/trf/downloads/trf407b.linux64 mv trf407b.linux64 ~/virtualenv/mgescan/bin/trf chmod 700 ~/virtualenv/mgescan/bin/trf ``` #### RepeatMasker ```sh 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 ------------------------------------------------------------------------------- ```sh git clone https://github.com/MGEScan/mgescan.git cd mgescan python setup.py install ``` ### virtualenv (optional for individual without sudo) ```sh virtualenv ~/virtualenv/mgescan source ~/virtualenv/mgescan/bin/activate ``` ### Galaxy modification ```sh cd ~/ cp -pr ~/mgescan/galaxy-modified/* ~/galaxy ``` ### Start Galaxy ```sh cd ~/galaxy ./run.sh & ``` Default port number : **38080** http://[IP ADDRESS]:38080 Command Line Tool (mgescan) ------------------------------------------------------------------------------- ```sh Usage: mgescan both [--output=] [--mpi=] mgescan ltr [--output=] [--mpi=] mgescan nonltr [--output=] [--mpi=] 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. ```sh (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](http://darwin.informatics.indiana.edu/cgi-bin/evolution/daphnia_ltr.pl) * [MGEScan-nonLTR](http://darwin.informatics.indiana.edu/cgi-bin/evolution/nonltr/nonltr.pl) 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 .

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