From 4a605e2c4a368f5c21a85ada2fb3f65229b2d165 Mon Sep 17 00:00:00 2001 From: kevinlibuit Date: Tue, 12 May 2020 16:42:27 -0400 Subject: [PATCH] clarify install confirmation --- README.md | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1c1bbadc..19876a62 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,24 @@ $ git clone https://github.com/StaPH-B/staphb_toolkit.git $ ./staphb_toolkit/setup.py ``` -Test the pipeline with the following command: +Test the pipeline with the following command and ensure you see the same usage output: ``` -$ staphb-tk test +$ staphb-tk +usage: staphb-tk [optional arguments] [application arguments] + +optional arguments: + -h, --help show this help message and exit + --docker_config , -c + Configuration file for container images and tags; if + none provided, default container versions will be + used. + --get_docker_config Get the default docker container configureation file. + --list, -l List all of the software available in the toolkit. + --update Check for and install a ToolKit update. + --auto_update Toggle automatic ToolKit updates. Default is off. + +custom program execution: + + mash_species MASH Species uses a custom database to identify the + isolate species. ```