From a4612e0cf7d848059ee024338543e3c2914762fe Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 18 Apr 2024 15:09:16 +0200 Subject: [PATCH] update readme --- README.md | 29 +++++++++++++++++++++++++---- src/task/api/task_info.yaml | 23 ++++++++++++++++++++++- 2 files changed, 47 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index d418c22e..6febe0d8 100644 --- a/README.md +++ b/README.md @@ -14,20 +14,41 @@ Path to source: ## Installation -You need to have Docker, Java, and Viash installed. Follow [these -instructions](https://openproblems.bio/documentation/fundamentals/requirements) +You need to have Docker, Java, and Viash installed. Follow +[these instructions](https://openproblems.bio/documentation/fundamentals/requirements) to install the required dependencies. ## First steps To get started, you can run the following commands: -``` bash +```bash git clone git@github.com:openproblems-bio/task-dge-perturbation-prediction.git cd task-dge-perturbation-prediction -scripts/sync_resources.sh +# download resources +scripts/download_resources.sh +``` + +To run the benchmark, you first need to build the components. Afterwards, you can run the benchmark: + +```bash +viash ns build --parallel --setup cachedbuild + +scripts/run_benchmark.sh +``` + +After adding a component, it is recommended to run the tests to ensure that the component is working correctly: + +```bash +viash ns test --parallel +``` + +Optionally, you can provide the `--query` argument to test only a subset of components: + +```bash +viash ns test --parallel --query "component_name" ``` ## Motivation diff --git a/src/task/api/task_info.yaml b/src/task/api/task_info.yaml index bfedc9f4..ccef9ad0 100644 --- a/src/task/api/task_info.yaml +++ b/src/task/api/task_info.yaml @@ -16,8 +16,29 @@ readme: | git clone git@github.com:openproblems-bio/task-dge-perturbation-prediction.git cd task-dge-perturbation-prediction + + # download resources + scripts/download_resources.sh + ``` + + To run the benchmark, you first need to build the components. Afterwards, you can run the benchmark: + + ```bash + viash ns build --parallel --setup cachedbuild + + scripts/run_benchmark.sh + ``` - scripts/sync_resources.sh + After adding a component, it is recommended to run the tests to ensure that the component is working correctly: + + ```bash + viash ns test --parallel + ``` + + Optionally, you can provide the `--query` argument to test only a subset of components: + + ```bash + viash ns test --parallel --query "component_name" ``` motivation: | Human biology can be complex, in part due to the function and interplay of the body's