From a8263b284768094d1df44a0bd32385fe38612756 Mon Sep 17 00:00:00 2001 From: Paula Ruiz-Rodriguez <50167687+Paururo@users.noreply.github.com> Date: Fri, 30 Oct 2026 11:49:24 +0100 Subject: [PATCH 1/2] docs: install from Bioconda, with its version and downloads in the README Recore is on Bioconda for Linux and macOS, Intel and ARM, so the README shows the Bioconda version and downloads and leads its install section with one conda command that brings minimap2 along. SECURITY.md now supports the Bioconda package instead of saying there is none. --- .github/SECURITY.md | 11 ++++++----- CHANGELOG.md | 4 ++++ README.md | 21 +++++++++++++++++---- 3 files changed, 27 insertions(+), 9 deletions(-) diff --git a/.github/SECURITY.md b/.github/SECURITY.md index 262b9e7..5afa6b3 100644 --- a/.github/SECURITY.md +++ b/.github/SECURITY.md @@ -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 diff --git a/CHANGELOG.md b/CHANGELOG.md index a3f754b..ecc0b5a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,10 @@ 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 and leads its + install section with that command, 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 diff --git a/README.md b/README.md index 15975a3..a5a73b4 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,8 @@ puts back the genes that are really there, and keeps the evidence for each one. License: AGPLv3 Rust 1.85+ DOI 10.5281/zenodo.23448590 +Bioconda version +Bioconda downloads @@ -42,16 +44,27 @@ __and Mireia Coscolla1__ ## 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 From 5b3381020ec2d900f0507b29c94e875b1e6f5d61 Mon Sep 17 00:00:00 2001 From: Paula Ruiz-Rodriguez <50167687+Paururo@users.noreply.github.com> Date: Fri, 30 Oct 2026 20:01:56 +0100 Subject: [PATCH 2/2] docs: lead the website's install section with Bioconda too The Install section now starts with the same one conda command as the README, which brings minimap2 along, and keeps minimap2 plus cargo as the source build beside it. --- CHANGELOG.md | 5 +++-- docs/index.html | 14 ++++++++------ 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ecc0b5a..a5f41b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,8 +18,9 @@ and Recore uses semantic versioning. - 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 and leads its - install section with that command, and `SECURITY.md` supports the package. + 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 diff --git a/docs/index.html b/docs/index.html index 6b141b8..94b577a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -75,11 +75,16 @@

Missing from the matrix. Still in the genome.

1

Install

-

Two commands. Recore uses minimap2 to search.

+

One command. Bioconda installs Recore together with minimap2, which it uses to search.

-
minimap2
+
Bioconda
+ 
$ conda install -c conda-forge -c bioconda recore
+

Linux and macOS, Intel and ARM. Check with recore --version. The package is on Bioconda.

+
+
+
Or from source: minimap2, then Recore
@@ -94,11 +99,8 @@

Install

-
-
-
Recore
$ cargo install --git https://github.com/PathoGenOmics-Lab/recore --locked
-

Needs Rust 1.85 or newer (rustup.rs), about a minute to build. Check with recore --version. The source is on GitHub.

+

Needs Rust 1.85 or newer (rustup.rs), about a minute to build. The source is on GitHub.