From d2cea748224fb6264c5ed97e224321956e70884f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Tue, 17 Dec 2024 16:54:22 +0100 Subject: [PATCH 1/4] fix: lean up documentation --- .streamlit/example.secrets.toml | 1 - README.md | 29 +++++++++++++++++------------ 2 files changed, 17 insertions(+), 13 deletions(-) diff --git a/.streamlit/example.secrets.toml b/.streamlit/example.secrets.toml index c3bade2..ea7c907 100644 --- a/.streamlit/example.secrets.toml +++ b/.streamlit/example.secrets.toml @@ -1,4 +1,3 @@ -# .streamlit/secrets.toml [aws] AWS_ACCESS_KEY_ID = "xxx" AWS_SECRET_ACCESS_KEY = "xxx" diff --git a/README.md b/README.md index bc8841e..cd52aaa 100644 --- a/README.md +++ b/README.md @@ -53,23 +53,28 @@ The current deployment of this project can be accessed at [biohack24.g15n.net](h cd vpipe-biohack24-frontend ``` -2. Build the Docker image: - ```sh - docker build -t vpipe-frontend . +2. Create a `.secrets.toml` file in the `.streamlit` directory with your AWS credentials and S3 bucket information: + ```env + AWS_ACCESS_KEY_ID=your_access_key_id + AWS_SECRET_ACCESS_KEY=your_secret_access_key + S3_BUCKET_NAME=your_s3_bucket_name ``` -3. Run the Docker container: - ```sh - docker run -p 8000:8000 --env-file .env vpipe-frontend +3. Configure the server IP addresses to LAPIS API for clinical and wastewater data in `confi.yaml` including ports: + ```env + server: + ip_address: "http://3.71.80.16:8000" + lapis_address: "http://3.126.120.246:8080" ``` -### Configuration +4. Build the Docker image: + ```sh + docker build -t vpipe-frontend . + ``` -1. Create a `.env` file in the root directory with your AWS credentials and S3 bucket information: - ```env - AWS_ACCESS_KEY_ID=your_access_key_id - AWS_SECRET_ACCESS_KEY=your_secret_access_key - S3_BUCKET_NAME=your_s3_bucket_name +5. Run the Docker container: + ```sh + docker run -p 8000:8000 vpipe-frontend ``` ### Usage From 49fa45fd1659f93b5933085a18e8ccf64a7593b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Tue, 17 Dec 2024 16:56:16 +0100 Subject: [PATCH 2/4] typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cd52aaa..3c74603 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,7 @@ The current deployment of this project can be accessed at [biohack24.g15n.net](h S3_BUCKET_NAME=your_s3_bucket_name ``` -3. Configure the server IP addresses to LAPIS API for clinical and wastewater data in `confi.yaml` including ports: +3. Configure the server IP addresses to LAPIS API for clinical and wastewater data in `config.yaml` including ports: ```env server: ip_address: "http://3.71.80.16:8000" From 98178e1eefa297243aab89230b019a52655758da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Tue, 17 Dec 2024 16:58:25 +0100 Subject: [PATCH 3/4] update content --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3c74603..3fa49da 100644 --- a/README.md +++ b/README.md @@ -7,8 +7,10 @@ ![AWS S3](https://img.shields.io/badge/AWS%20S3-Cloud-orange) This project provides a front-end interface for two primary use cases: -- On-demand heatmaps of mutations to identify new variants emerging. -- On-demand variant deconvolution powered by Lollipop. +- On-demand heatmaps of mutations to identify new variants emerging, based on V-Pipe outputs. +- On-demand variant deconvolution powered by LolliPop. +- On-demand heatmaps of resistance mutation – querying LAPIS of clincial data. +- On-demand heatmaps of reistance mutations - querying LAPS of wastewater data. ## Overview From 6ad1a1f35d17736923b6a0015ed4705657e14ea6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Tue, 17 Dec 2024 16:58:50 +0100 Subject: [PATCH 4/4] update content --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3fa49da..7762c43 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ This project provides a front-end interface for two primary use cases: - On-demand heatmaps of mutations to identify new variants emerging, based on V-Pipe outputs. - On-demand variant deconvolution powered by LolliPop. - On-demand heatmaps of resistance mutation – querying LAPIS of clincial data. -- On-demand heatmaps of reistance mutations - querying LAPS of wastewater data. +- On-demand heatmaps of resistance mutations - querying LAPS of wastewater data. ## Overview