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Submodule common
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@@ -2,52 +2,6 @@ name: A unique identifier. Can only contain lowercase letters, numbers or unders | |
label: A unique, human-readable, short label. Used for creating summary tables and visualisations. | ||
summary: A one sentence summary of purpose and methodology. Used for creating an overview tables. | ||
image: The name of the image file to use for the component on the website. | ||
readme: | | ||
## Installation | ||
You need to have Docker, Java, and Viash installed. Follow | ||
[these instructions](https://openproblems.bio/documentation/fundamentals/requirements) | ||
to install the required dependencies. | ||
## Add a method | ||
To add a method to the repository, follow the instructions in the `scripts/add_a_method.sh` script. | ||
## Frequently used commands | ||
To get started, you can run the following commands: | ||
```bash | ||
git clone [email protected]:openproblems-bio/task_<task-name>.git | ||
cd <task-name> | ||
# initialise submodule | ||
scripts/init_submodule.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: | | ||
Explain the motivation behind your proposed task. Describe the biological or computational | ||
problem you aim to address and why it’s important. Discuss the current state of research in | ||
|