diff --git a/README.md b/README.md index b64513f..17ebc71 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,7 @@ cd /path/to/Cryo-EM-Heterogeneity-Challenge-1 pip install . ``` -## Devel installation +## Developer installation If you are interested in testing the programs previously installed, please, install the repository in development mode with the following commands: ```bash @@ -52,6 +52,7 @@ The test included in the repo can be executed with PyTest as shown below: ```bash cd /path/to/Cryo-EM-Heterogeneity-Challenge-1 +sh tests/scripts/fetch_test_data.sh # download test data from OSF pytest tests/test_preprocessing.py pytest tests/test_svd.py pytest tests/test_map_to_map.py @@ -59,9 +60,14 @@ pytest tests/test_distribution_to_distribution.py ``` # Running -If you want to run our code, please check the notebooks in the [tutorials folder](https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/tree/main/tutorials). +If you want to run our code on the full challenge data, or you own local data, please complete the following steps -The tutorials explain how to setup the config files, and run the commands +### 1. Dowload the full challenge data from [The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge](https://osf.io/8h6fz/) +You can do this through the web browser, or programatically with wget (you can get inspiration from [this script](https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/blob/main/tests/scripts/fetch_test_data.sh), which is just for the test data, not the full datasets) + +### 2. Modify the config files and run the commands on the full challenge data +Point to the path where the data is locally +The [tutorial notebooks](https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/tree/main/tutorials) explain how to setup the config files, and run the commands ``` cryo_challenge run_preprocessing --config config_files/config_preproc.yaml cryo_challenge run_svd --config config_files/config_svd.yaml @@ -69,6 +75,7 @@ cryo_challenge run_map2map_pipeline --config config_files/conf cryo_challenge run_distribution2distribution_pipeline --config config_files/config_distribution_to_distribution.yaml ``` + # Contributing If you find any bug or have a suggestion on the code feel free to open an issue [here](https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/issues).