MIRA-Oxide

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Overview

MIRA-Oxide is a RUST package that is utilized by MIRA-NF to perform assembly and annotation of Influenza genomes, SARS-CoV-2 genomes, the SARS-CoV-2 spike-gene and RSV genomes.

Subprocesses

MIRA-Oxide has standalone subprocesses within it that perform different tasks. These are run on their own with

mira-oxide <SUBPROCESS> [subprocess arguments]

Current subprocesses include:

• Hamming Distance between all samples
• Nucleotide Diffs between all samples
• Find Chemistry, for selecting the correct module and configs for IRMA
• Plotter, for plotting,
• Variants of Interest, for taking DAIS-ribosome outputs and a list of sequences to find mutations that will cause variants

Each subprocess has its own README, found in docs/.

Adding New Subprocess to MIRA-Oxide

Before starting be sure that you have rust nightly installed and set as default. You will also need to have Cargo installed. If you need more information about how to install those, see here.

If you are using VScode the rust-analyzer extension is very help with formatting and debugging.

Step 1

Clone the repository.

git clone https://github.com/CDCgov/mira-oxide.git

Step 2

Move into the folder made by Cargo and create new branch for your subprocess.

cd mira-oxide
git checkout -b add_new_subprocess_name

Step 3

Mira-oxide requires rust-nightly to run the zoe crate.

Install the nightly version of rust.

rustup toolchain install nightly

Using nightly for mira-oxide

rustup override set nightly

Step 4

touch src/processes/subprocess_name.rs

1. Create a new process under src/processes

2. Add that process to src/processs/mod.rs by editing mod.rs with pub mod subprocess_name;

3. Import the file in src/main.rs by adding the subprocess to the list: use crate::processes::{[other processes], subprocess_name::*};

4. Add your subprocess to the enum Commands

Step 5

Start Working!

1. Work on your subprocess in src/processes/subprocess_name.rs. You can add a new struct with specific arguments for this process: pub struct ProcessArgs.
2. You should should have a "main" function called something like pub fn name_process(args: ProcessArgs). It can call off to helper functions in the same file, or for shared functionality, something in src/utils
3. Once you have created the name_process(args) function, add it to the match statement in main.rs.

Step 6

Run your program!

To be sure that your package is working within the workspace go the workspace area (path-to-repo-folder/mira-oxide) and run this command:

cargo run -- <SUBPROCESS-NAME> [SUBPROCESS ARGS]

Or, if it is compiled, you can find the debug or release binary in the target/ directory, and run it directly via

./target/debug/mira-oxide <SUBPROCESS-NAME> [SUBPROCESS ARGS]

Step 7

Provide usage documentation.

Create a README.md within the docs/ folder. Within that README provide a description of the subprocess, its inputs, its outputs and how to execute it.

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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.

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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.

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

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