From 6dca885da90d2cd83f8e6f233990a20a85b2d1a4 Mon Sep 17 00:00:00 2001 From: Arjun Prasad Date: Sat, 16 Nov 2024 07:11:54 -0500 Subject: [PATCH] Docs point to dockerhub and AMRFinderPlus Updated with info about StxTyper in the ncbi/amr dockerhub image and that it is installed along with AMRFinderPlus. --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 21162cd..626a206 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,8 @@ StxTyper is used to determine stx type from nucleotide sequence. Stx (Shiga-toxi # Installation +Note StxTyper is included with [AMRFinderPlus](https://github.com/ncbi/amr/wiki) as of version 4.0 and is run by AMRFinderPlus when the `--organism Escherichia option is used`. If you have installed AMRFinderPlus you don't need to separately install StxTyper. + ## Installing with Bioconda You'll need Mamba ([Installation instructions](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)) first. @@ -67,6 +69,9 @@ StxTyper should compile cleanly for Mac and Linux x86 and ARM, though our offici make make test +## Docker + +StxTyper is included with several Docker images including the [ncbi/amr](https://hub.docker.com/r/ncbi/amr/) docker image. # Usage