fqtk

A toolkit for working with FASTQ files, written in Rust.

Installing

Installing with conda

To install with conda you must first install conda. Then, in your command line (and with the environment you wish to install fqtk into active) run:

console conda install -c bioconda fqtk

Installing with cargo

To install with cargo you must first install rust. Which (On Mac OS and Linux) can be done with the command:

console curl https://sh.rustup.rs -sSf | sh

Then, to install fqtk run:

console cargo install fqtk

Building From Source

First, clone the git repo:

console git clone https://github.com/fulcrumgenomics/fqtk.git

Secondly, if you do not already have rust development tools installed, install via rustup:

console curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

Then build the toolkit in release mode:

console cd fqtk cargo build --release ./target/release/fqtk --help

Developing

fqtk is developed in Rust and follows the conventions of using rustfmt and clippy to ensure both code quality and standardized formatting. When working on fqtk, before pushing any commits, please first run ./ci/check.sh and resolve any issues that are reported.

Releasing a New Version

Pre-requisites

Install cargo-release

console cargo install cargo-release

Prior to Any Release

Create a release that will not try to push to crates.io and verify the command:

console cargo release [major,minor,patch,release,rc...] --no-publish

Note: "dry-run" is the default for cargo release.

See the cargo-release reference documentation for more information

Semantic Versioning

This tool follows Semantic Versioning. In brief:

• MAJOR version when you make incompatible API changes,
• MINOR version when you add functionality in a backwards compatible manner, and
• PATCH version when you make backwards compatible bug fixes.

Major Release

To create a major release:

console cargo release major --execute

This will remove any pre-release extension, create a new tag and push it to github, and push the release to creates.io.

Upon success, move the version to the next candidate release.

Finally, make sure to create a new release on GitHub.

Minor and Patch Release

To create a minor (patch) release, follow the Major Release instructions substituting major with minor (patch):

console cargo release minor --execute

Release Candidate

To move to the next release candidate:

console cargo release rc --no-tag --no-publish --execute

This will create or bump the pre-release version and push the changes to the main branch on github. This will not tag and publish the release candidate. If you would like to tag the release candidate on github, remove --no-tag to create a new tag and push it to github.