You can run pipeline through

1. Clone git repository

2. Dockerimage without clone repository

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

module load Python/3.7

module load ncbi-blast+/LATEST

module load muscle/3.8.425

module load raxml/8.2.9

module load Entrez/E-utilities

module load prodigal/2.63

pip install -r requirements.txt --user

git clone https://github.com/CDCgov/lpsubp.git

cd ~/lpsubp/

python pipe1.py ~/50scheme/test1/

module load singularity

singularity pull docker:https://supark87/dockerfile_gittest

singularity run -B $(pwd)/inputfile/:https://data/inputfile/(space here)dockerfile_gittest.simg(spacehere)//data/inputfile

docker pull supark87/dockerfile_gittest

docker run -it -v $(pwd)/inputfile/:/data/inputfile/ supark87/dockerfile_gittest /data/inputfile/ "your email inside of quotes"

This script runs entire pipeline from the beginning and get all output results

*base_dir: type 'pwd' in your home directory(i.e./scicomp/home/youruserid/)

There would be "outputfile" directory at the end of pipeline under "your_home_directory/your_genome_directory" (i.e./scicomp/home/youruserid/test1/outputfile/)

There would be myscript.log in your home directory that you can check when the pipeline started, each step completed, and finished.

Subin Park

APHL fellow at Centers for Disease control and Prevention

Phone : +1 470 725 5110 Email :[email protected]

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The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later. This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version. This source code in this repository 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 Apache Software License for more details. You should have received a copy of the Apache Software License along with this program. If not, see https://www.apache.org/licenses/LICENSE-2.0.html The source code forked from other open source projects will inherit its license.

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All comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at https://www.cdc.gov/other/privacy.html.

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Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.