redskull

A conda recipe generator for Rust crates, written in Rust.

Visit us at Fulcrum Genomics to learn more about how we can power your Bioinformatics with redskull and beyond.

redskull: "grayskull for Rust".

redskull is a conda recipe generator for rust recipes.

Usage for redskull follows:

OVERVIEW

redskull: grayskull for rust.

Specify the crates.io packages name. Redskull can also accept a github url.

Usage: redskull [OPTIONS] [ARGS]...

Arguments:
  [ARGS]...
          Crates.io package names or GitHub URLs

Options:
      --maintainers <MAINTAINERS>
          List of maintainers which will be added to the recipe

      --output <OUTPUT>
          Path to where the recipe will be created

  -r, --recursive
          Recursively run grayskull on missing dependencies

      --tag <GITHUB_RELEASE_TAG>
          If tag is specified, Redskull will build from release tag

      --crate-version <CRATE_VERSION>
          Override the crate version (defaults to the latest version on crates.io)

      --bioconda
          Add additional output for bioconda compatibility

      --cargo-bundle-licenses <CARGO_BUNDLE_LICENSES>
          Use cargo-bundle-licenses to generate THIRDPARTY.yml. Defaults to true when --bioconda is set, unless explicitly disabled

          [possible values: true, false]

      --host-dep <HOST_DEP>
          Override: additional host dependencies (e.g., --host-dep zlib --host-dep openssl)

      --run-dep <RUN_DEP>
          Override: additional run dependencies (e.g., --run-dep samtools --run-dep minimap2)

      --test-command <TEST_COMMAND>
          Override: test commands (e.g., --test-command "mytool --version")

      --skip-platform <SKIP_PLATFORM>
          Override: skip platforms (e.g., --skip-platform osx)

      --recipe-name <RECIPE_NAME>
          Override the recipe name (defaults to the crates.io package name). Useful when the bioconda recipe name differs from the crate name

      --source <SOURCE>
          Source type: "github" (default) or "crates-io"

          [default: github]

          Possible values:
          - github:    Use GitHub release archives (default)
          - crates-io: Use crates.io tarballs

      --max-pin <MAX_PIN>
          Override the max_pin value for run_exports (default: "x.x"). Use "x" for pre-1.0 tools

      --refs-tags
          Use refs/tags/ in GitHub archive URL template. Both forms resolve identically on GitHub; this controls the template text

      --cargo-net-git-fetch
          Set CARGO_NET_GIT_FETCH_WITH_CLI=true in build.sh. Needed when the build environment requires SSH for git fetches

      --test-version
          Use --version instead of --help for auto-generated test commands

      --strip
          Strip debug symbols from binaries after build

      --license-family <LICENSE_FAMILY>
          Emit license_family in the recipe. Defaults to true

          [possible values: true, false]

      --identifier <IDENTIFIER>
          Add identifiers to the extra section (e.g., --identifier "doi:10.1234/foo")

      --workspace-path <WORKSPACE_PATH>
          Override workspace member path (e.g., --workspace-path crates/cmdline)

  -h, --help
          Print help (see a summary with '-h')

  -V, --version
          Print version

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 redskull into active) run:

conda install -c bioconda redskull

Installing with cargo

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

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

Then, to install redskull run:

cargo install redskull

Building From Source

First, clone the git repo:

git clone https://github.com/fg-labs/redskull.git

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

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

Then build the toolkit in release mode:

cd redskull
cargo build --release
./target/release/redskull --help

Developing

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

Releasing a New Version

Releases are automated with release-plz, driven by Conventional Commits on main.

How it works

On every push to main, the release-plz workflow (.github/workflows/release-plz.yml) runs and does two things:

1. Opens or updates a release PR that bumps the version in Cargo.toml and Cargo.lock and updates CHANGELOG.md based on commit messages since the last tag.
2. Publishes to crates.io and creates a GitHub release when a release PR is merged, tagging the commit and pushing the crate to crates.io.

Conventional Commits

The version bump is derived from commit messages since the last release:

• feat: — minor bump (new functionality)
• fix: — patch bump (bug fix)
• feat!: or BREAKING CHANGE: — major bump (incompatible change)
• chore:, docs:, refactor:, test:, ci: — no bump on their own

This tool follows Semantic Versioning.

Cutting a release

1. Merge your changes to main using Conventional Commit messages.
2. Review the release PR opened by release-plz (version bump + changelog).
3. Merge the release PR. release-plz publishes to crates.io and creates the GitHub release automatically.

Publishing credentials: Trusted Publishing

This repository uses crates.io Trusted Publishing (OIDC) instead of a long-lived CARGO_REGISTRY_TOKEN secret. The release-plz workflow requests a short-lived token from crates.io via GitHub's OIDC provider at publish time — nothing needs to be stored in the repository.

The workflow already sets id-token: write on the release job, which is required for OIDC.

First release

Trusted Publishing cannot be used for the first version of a new crate — the 0.1.0 release must be published manually:

cargo login                 # with a short-lived API token from https://crates.io/settings/tokens
cargo publish
cargo logout

Then tag the release on GitHub and delete the API token.

Subsequent releases

After 0.1.0 is on crates.io, configure a Trusted Publisher for this repository under crates.io → Settings → Trusted Publishing:

• Repository owner: fg-labs
• Repository name: redskull
• Workflow filename: release-plz.yml
• Environment: (leave blank)

Once configured, merging a release PR on main will publish automatically.