Mia: Mobile influenza analysis

This repository was created for use by CDC programs to collaborate on public health surveillance related projects in support of the CDC Surveillance Strategy. Github is not hosted by the CDC, but is used by CDC and its partners to share information and collaborate on software.

This repository contains scripts used for the manuscript Mitigating Pandemic Risk with Influenza Virus A Field Survillance at a Swine-Human Interface currently available at BioRxiv and in submission for peer-review publication. This is currently a beta version and requires substantial dependencies. A containerized version is under active development and when available, a redirect will be available here.

Installation

bash git clone https://github.com/CDCgov/Mia_publication.git cd MIA/scripts sudo bash install.sh cd -

Dependencies

Everything below is attempted to install with ./MIA/scripts/install.sh. Due to the large number of dependencies however, there is a decent chance everything will not properly install, requiring some manual troubleshooting/install. Setting up the R environment can be particularly sticky.

Python 3.5 and 2.7

bash sudo apt-get install python3.5 sudo apt-get install python2.7

MinKnow

bash sudo apt-get update sudo apt-get install wget wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add - echo "deb http://mirror.oxfordnanoportal.com/apt xenial-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list sudo apt-get update sudo apt-get install minknow-nc

Guppy

bash sudo apt-get update sudo apt-get install wget lsb-release export PLATFORM=$(lsb_release -cs) wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add - echo "deb http://mirror.oxfordnanoportal.com/apt ${PLATFORM}-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list sudo apt-get update

Aliview

bash cd bin wget http://www.ormbunkar.se/aliview/downloads/linux/linux-version-1.26/aliview.install.run chmod +x sudo ./aliview.install.run cd -

inotifywait

bash sudo apt-get install inotify-tools

IRMA: Iterative Refinement MetaAssembler

IRMA is prepackaged within Mia's repository and should work without requiring the following install: bash cd bin wget https://wonder.cdc.gov/amd/flu/irma/flu-amd.zip unzip flu-amd.zip cd -

BLAST+

BLAST+ is prepackaged within Mia's repository and should work without requiring the following install: bash cd lib wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz tar -xzf ncbi-blast-2.9.0+-x64-linux.tar.gz cd -

FastTree Double Precision

bash cd bin wget http://www.microbesonline.org/fasttree/FastTreeDbl cd -

Muscle

Muscle is prepackaged within Mia's repository and should work without requiring the following install: bash cd bin wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz tar -xzf muscle3.8.31_i86linux64.tar.gz cd -

SQLite

Install SQLite

R

```bash cd bin wget https://mran.blob.core.windows.net/install/mro/3.5.3/ubuntu/microsoft-r-open-3.5.3.tar.gz tar -xf microsoft-r-open-3.5.3.tar.gz sudo microsoft-r-open/install.sh

Follow prompts

cd - ```

R dependencies

bash sudo Rscript ./scripts/install_R_libs.R

Build database and initialize references

bash cd scripts bash createMIAdb.sh cd -

Create Desktop Icon

bash cd scripts bash makeDesktopIcon.sh cd -

Set crontab

bash cd scripts bash setCron.sh cd -

Public Domain

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License

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 http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

Privacy

This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/privacy.html.

Contributing

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

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 http://www.cdc.gov/other/privacy.html.

Records

This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.

Notices

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