From 23a995c3c4ee6c2ea0a809083c4cb7bdc9d97f40 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Aug 2026 15:02:21 +0200 Subject: [PATCH] Correct the stale parts of the README - The minimum Rust version was given as 1.35. The real floor is 1.88, set by the icu crates that come in through attohttpc -> url -> idna. - The crate was never mentioned, even though it has been on crates.io since 2019 with over 6000 downloads. Added `cargo install umgap`, noting that it installs only the binary: the pipeline scripts are not part of the published crate, so the clone is still needed for those. - The metagenomics case study link pointed at /clidocs/casestudies/metagenomics, which is not a route on the website. It lives at /umgap/casestudies. - The visualisation step was marked NOT YET INTEGRATED and showed a command that does not match the script's interface. It takes -w and writes to standard output. Co-Authored-By: Claude Opus 5 --- README.md | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 72ea09e9..c7c967e1 100644 --- a/README.md +++ b/README.md @@ -12,10 +12,12 @@ Statistics at [Ghent University]. 1. Install [Rust], according to [their installation instructions][rust-install], or use your favourite package manager (e.g. `apt install rustc`). The - pipeline is developed for the latest stable release, but should work on 1.35 - and higher. + pipeline is developed for the latest stable release and needs at least Rust + 1.88. -2. Clone this repository and go to the repository root. +2. Clone this repository and go to the repository root. The preconfigured + pipelines and the setup script live here; they are not part of the published + crate. ```sh git clone https://github.com/unipept/umgap.git @@ -29,6 +31,13 @@ Statistics at [Ghent University]. cargo install --path . ``` + If you only need the `umgap` command itself and not the pipeline scripts, + you can skip the clone and install it from [crates.io][crate] instead: + + ```sh + cargo install umgap + ``` + For a multiuser installation, instead of `cargo install`, use `install` to place the umgap program and the wrapper script were all users can reach it: @@ -73,10 +82,10 @@ Statistics at [Ghent University]. ./scripts/umgap-analyse.sh -1 testdata/A1.fq -2 testdata/A2.fq -o - | tee output.fa ``` -7. (optional) NOT YET INTEGRATED - Visualize some test data! Running +7. (optional) Visualize some test data! Running ```sh - ./scripts/umgap-visualize.sh output.fa output.html + ./scripts/umgap-visualize.sh -w output.fa > output.html ``` will give you an HTML-file, which will show you a visualization of the test @@ -133,7 +142,8 @@ for more info. [Unipept]: https://unipept.ugent.be/ [Ghent University]: https://www.ugent.be/ [Rust]: https://www.rust-lang.org/ -[metagenomics casestudy]: https://unipept.ugent.be/clidocs/casestudies/metagenomics +[metagenomics casestudy]: https://unipept.ugent.be/umgap/casestudies +[crate]: https://crates.io/crates/umgap [rust-install]: https://www.rust-lang.org/tools/install [FragGeneScanPlusPlus]: https://github.com/unipept/FragGeneScanPlusPlus [EditorConfig]: https://editorconfig.org/