Correct the stale parts of the README - #12
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- 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 <noreply@anthropic.com>
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Four things in the README that no longer hold. Each was checked against the current tooling rather than read off the page.
icucrates viaattohttpc->url->idna. The MSRV job in #10 builds against exactly this.cargo install umgapwas undocumented. It installs only the binary and none ofscripts/, so the README now says the clone is still needed for the preconfigured pipelines.[metagenomics casestudy]->/clidocs/casestudies/metagenomics/umgap/casestudies.umgap-visualize.sh output.fa output.html"-w, writing to stdout. The command shown was never its interface.The gene predictor is handled separately in #13, which swaps FragGeneScan++ for FragGeneScanRs. The two touch disjoint parts of the README and merge cleanly in either order; I verified that locally.
Worth knowing
cargo install umgaptoday gets 1.1.0, which still has thejoinkmersbug from #8. Either hold this until 1.1.1 is published, or merge and accept a short window.umgap-visualize.sh -tfails on macOS withfind: -printf: unknown primary or operator, a GNU-only flag. Not touched here.