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11 changes: 6 additions & 5 deletions .github/SECURITY.md
Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,12 @@ There is deliberately no backport branch. A security fix goes onto `main` and
out in the next release, and the answer to "which version should I run" is the
newest one.

Nothing else is supported. In particular there is no Bioconda package, no
container image and no third-party build maintained by this project, so a binary
you did not build yourself or download from this repository's
[Releases](https://github.com/PathoGenOmics-Lab/recore/releases) page is outside
what we can speak for.
The [Bioconda package](https://anaconda.org/bioconda/recore) is built from the
release tarballs and supported like the release it carries. Nothing else is:
there is no container image or other third-party build maintained by this
project, so a binary you did not build yourself, download from this
repository's [Releases](https://github.com/PathoGenOmics-Lab/recore/releases)
page or install from Bioconda is outside what we can speak for.

## What counts as a vulnerability here

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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,11 @@ and Recore uses semantic versioning.

### Added

- Recore is on Bioconda for Linux and macOS, Intel and ARM:
`conda install -c conda-forge -c bioconda recore` installs it together with
minimap2. The README shows the Bioconda version and downloads, the README and
the website's Install section lead with that command and keep the source
build as the alternative, and `SECURITY.md` supports the package.
- Recore is archived on Zenodo. The README carries the DOI badge and both DOIs
(10.5281/zenodo.23448590 for every version, 10.5281/zenodo.23448591 for 1.0.0), `CITATION.cff` holds
them, the citation page has a BibTeX entry for the software, and the
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21 changes: 17 additions & 4 deletions README.md
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Expand Up @@ -24,6 +24,8 @@ puts back the genes that are really there, and keeps the evidence for each one.
<a href="LICENSE"><img src="https://img.shields.io/badge/license-AGPLv3-blue.svg" alt="License: AGPLv3"></a>
<img src="https://img.shields.io/badge/Rust-1.85%2B-orange.svg" alt="Rust 1.85+">
<a href="https://doi.org/10.5281/zenodo.23448590"><img src="https://img.shields.io/badge/doi-10.5281%2Fzenodo.23448590-%23ff0077" alt="DOI 10.5281/zenodo.23448590"></a>
<a href="https://anaconda.org/bioconda/recore"><img src="https://img.shields.io/conda/vn/bioconda/recore?label=bioconda&color=009E73" alt="Bioconda version"></a>
<a href="https://anaconda.org/bioconda/recore"><img src="https://img.shields.io/conda/dn/bioconda/recore?label=downloads&color=009E73" alt="Bioconda downloads"></a>

</div>

Expand All @@ -42,16 +44,27 @@ __and Mireia Coscolla<sup>1</sup>__

## 1 · Install

Two commands. Recore uses [minimap2](https://github.com/lh3/minimap2) to search.
One command. [Bioconda](https://anaconda.org/bioconda/recore) installs Recore
together with [minimap2](https://github.com/lh3/minimap2), which it uses to
search, on Linux and macOS, Intel and ARM alike.

```bash
conda install -c conda-forge -c bioconda recore
```

Check with `recore --version`.

To build it from source instead, you need Rust 1.85 or newer
([rustup.rs](https://rustup.rs)) and minimap2 on your `PATH`; the build takes
about a minute.

```bash
conda install -c bioconda minimap2 # or: brew install minimap2 / sudo apt install minimap2
cargo install --git https://github.com/PathoGenOmics-Lab/recore --locked
```

Needs Rust 1.85 or newer ([rustup.rs](https://rustup.rs)), about a minute to
build. Check with `recore --version`. From a clone, `cargo build --release`
puts the binary at `target/release/recore`.
From a clone, `cargo build --release` puts the binary at
`target/release/recore`.

## 2 · Your command

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14 changes: 8 additions & 6 deletions docs/index.html
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Expand Up @@ -75,11 +75,16 @@ <h1>Missing from the matrix. <span class="grad">Still in the genome.</span></h1>
<div class="section-head">
<span class="num">1</span>
<h2>Install</h2>
<p>Two commands. Recore uses minimap2 to search.</p>
<p>One command. Bioconda installs Recore together with minimap2, which it uses to search.</p>
</div>
<div class="cols-2">
<div class="card">
<div class="step-label">minimap2</div>
<div class="step-label">Bioconda</div>
<div class="code one-line"><pre><span class="p">$ </span>conda install -c conda-forge -c bioconda recore</pre></div>
<p class="note">Linux and macOS, Intel and ARM. Check with <code>recore --version</code>. The package is <a href="https://anaconda.org/bioconda/recore">on Bioconda</a>.</p>
</div>
<div class="card">
<div class="step-label">Or from source: minimap2, then Recore</div>
<div class="tabs" role="tablist" aria-label="Install minimap2 with">
<button class="tab" role="tab" aria-selected="true" aria-controls="mm-conda" id="mm-conda-tab">conda</button>
<button class="tab" role="tab" aria-selected="false" aria-controls="mm-brew" id="mm-brew-tab">Homebrew</button>
Expand All @@ -94,11 +99,8 @@ <h2>Install</h2>
<div class="tabpanel" role="tabpanel" id="mm-apt" aria-labelledby="mm-apt-tab" hidden>
<div class="code"><pre><span class="p">$ </span>sudo apt install minimap2</pre></div>
</div>
</div>
<div class="card">
<div class="step-label">Recore</div>
<div class="code one-line"><pre><span class="p">$ </span>cargo install --git https://github.com/PathoGenOmics-Lab/recore --locked</pre></div>
<p class="note">Needs Rust 1.85 or newer (<a href="https://rustup.rs">rustup.rs</a>), about a minute to build. Check with <code>recore --version</code>. The source is <a href="https://github.com/PathoGenOmics-Lab/recore">on GitHub</a>.</p>
<p class="note">Needs Rust 1.85 or newer (<a href="https://rustup.rs">rustup.rs</a>), about a minute to build. The source is <a href="https://github.com/PathoGenOmics-Lab/recore">on GitHub</a>.</p>
</div>
</div>
</div>
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