From 10a649493167ce1812954179af4859791dc0b701 Mon Sep 17 00:00:00 2001 From: tombch Date: Tue, 19 Sep 2023 15:44:50 +0100 Subject: [PATCH] Small updates to the install guide, and fixing GitHub hyperlink --- docs/onyx_client_installation_guide.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/onyx_client_installation_guide.md b/docs/onyx_client_installation_guide.md index 775979f..b7ae934 100644 --- a/docs/onyx_client_installation_guide.md +++ b/docs/onyx_client_installation_guide.md @@ -1,6 +1,6 @@ # Onyx Client Installation Guide -This guide walks through how to install the `onyx` client in a CLIMB Jupyter notebook. +This guide walks through how to install the Onyx client in a CLIMB Jupyter notebook. ## Download the client @@ -12,13 +12,13 @@ $ git clone https://github.com/CLIMB-COVID/onyx-client.git ## Install the client -Create a python virtual environment for the client: +Create a Python virtual environment for the client: ``` $ python -m venv onyx-env ``` -Install the `onyx` client within this environment: +Install the client within this environment: ``` $ source onyx-env/bin/activate @@ -27,7 +27,7 @@ $ source onyx-env/bin/activate ## Create a config -Create an `onyx` config folder with the `onyx config create` command. +Generate a config folder with the `onyx config create` command. For this you need to provide: @@ -44,7 +44,7 @@ Once this is done, you **must** export the environment variable `ONYX_CLIENT_CON ## Register -Register for an `onyx` account with the `onyx register` command. +Register for an Onyx account with the `onyx register` command. For this you need to provide: @@ -64,7 +64,7 @@ And then follow the instructions. ## Log in -To log in to your `onyx` account, run the following command and enter your password: +To log in to your Onyx account, run the following command and enter your password: ``` (onyx-env) $ onyx login @@ -114,11 +114,11 @@ To filter for all samples with a `published_date` within the dates `2023-09-01` ## Further guidance -For further guidance using the `onyx` client, use the `--help` option. +For further guidance using the Onyx client, use the `--help` option. ``` (onyx-env) $ onyx --help (onyx-env) $ onyx filter --help ``` -Or, check out the `README` file on the `onyx-client` GitHub page: https://github.com/CLIMB-TRE/onyx-client +Or, check out the README file on the Onyx client's [GitHub page](https://github.com/CLIMB-TRE/onyx-client).