From 3cb1f64d03fe250798b358a027b8ed3d63f69703 Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Thu, 27 Jun 2024 10:47:17 +0200
Subject: [PATCH] WIP instructions

---
 INSTRUCTIONS.md | 73 +++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 67 insertions(+), 6 deletions(-)

diff --git a/INSTRUCTIONS.md b/INSTRUCTIONS.md
index 74287af..dcb539e 100644
--- a/INSTRUCTIONS.md
+++ b/INSTRUCTIONS.md
@@ -2,16 +2,77 @@
 
 This is a guide on what to do after you have created a new task repository from the template. More in depth information about how to create a new task can be found in the [OpenProblems Documentation](https://openproblems.bio/documentation/create_task/).
 
+## Requirments
+
+A list of required software to start developing a new task can be found in the [OpenProblems Requirements](https://openproblems.bio/documentation/create_task/requirements).
+
 ## First things first
 
-* Update the `_viash.yaml` file with the correct task information.
-* Update the `src/api/task_info.yaml` file with the information you have provied in the task issue.
+### `_viash.yaml`
+
+* Update the `name` field to the name of the task in snake_case.
+* Update the `description` field to a short description of the task.
+* Add a keyword to the `keywords` field that describes the task.
+* Update the `<task_name>` in the links field to the name of the task in snake_case.
+
+### `task_info.yaml`
+
+
+* Update the `src/api/task_info.yaml` file with the information you have provided in the task issue.
+* Update the `<task_name>` in the `readme` field to the name of the task.
+
+### `common` submodule
+
+Initialize the `common` submodule by running the following command:
+
+```bash
+scripts/init_submodule.sh
+```
 
 ## Resources
 
-THe OpenProblems team has provided some test resources that can be used to test the task. These resources are stored in the `resources` folder. The `scripts/download_resources.sh` script can be used to download these resources.
+The OpenProblems team has provided some test resources that can be used to test the task. These resources are stored in the `resources_test` folder. The `scripts/download_resources.sh` script can be used to download these resources.
+If these resources are not sufficient, you can add more resources to the `resources_test` folder. The `scripts/download_resources.sh` script can be updated to download these resources. When using new test_resources let the OP team know so they can be added to the s3 bucket.
+
+```bash	
+scripts/download_resources.sh
+```
+
+## Next steps
+
+### API files ([docs](https://openproblems.bio/documentation/create_task/design_api))
+
+Update the API files in the `src/api` folder. These files define the input and output of the methods and metrics. 
+
+### Components ([docs](https://openproblems.bio/documentation/create_task/create_components))
+
+To create a component, you can run the respective script in the `script` directory. Before running the script make sure to update the variables `task_name`, `component_name` and `component_lang` and save the file. For additionale components ou will only need to update the `component_name` and `component_lang` variables.
+
+```bash
+scripts/add_a_control_method.sh
+```
+
+```bash
+scripts/add_a_method.sh
+```
+
+```bash
+scripts/add_a_metric.sh
+```
+
+For each type of component there already is a first component created that you can modify.
+
+1. Update the `.info` fields in the  `config.vsh.yaml`.
+2. Add any component specific arguments to the `config.vsh.yaml` file.
+3. Add any additional reqources that are required for the component.
+4. Update the docker engine image setup if additional packages are required.
+5. If you know the required memory and or CPU you can adjust the nextflow `.directive.labels` field. In addition if your component requires a GPU you can add the `gpu` label to the field.
+6. Update the `script.py` or `script.R` file with the code for the component.
+
+> [!NOTE]
+> You can remove the comments in the `config.vsh.yaml` file after you have updated the file.
+
 
-If these resources are not sufficient, you can add more resources to the `resources` folder. The `scripts/download_resources.sh` script can be updated to download these resources.
 
 
 
@@ -23,7 +84,7 @@ If these resources are not sufficient, you can add more resources to the `resour
 * update scripts/download_resources
 -->
 
-#!/bin/bash
+<!-- #!/bin/bash
 
 echo "This script is not supposed to be run directly."
 echo "Please run the script step-by-step."
@@ -70,4 +131,4 @@ viash run src/task/metrics/mean_rowwise_error/config.vsh.yaml -- \
   --output "output/score.h5ad"
 
 # print score on kaggle test dataset
-python -c 'import anndata; print(anndata.read_h5ad("output/score.h5ad").uns)'
\ No newline at end of file
+python -c 'import anndata; print(anndata.read_h5ad("output/score.h5ad").uns)' -->
\ No newline at end of file