Use new mitocheck data

0.download_data/README.md

@@ -2,16 +2,29 @@
 
 In this module, we present our method for downloading nucleus morphology data.
 
-## Download/Process Data
+### Download/Preprocess Data
 
-Complete instructions for data download and processing can be found at: https://github.com/WayScience/mitocheck_data
+Complete instructions for data download and preprocessing can be found at: https://github.com/WayScience/mitocheck_data
 
-## Usage
+### Usage
 
-In this repository, all training data is compiled from version controlled data from [mitocheck_data](https://github.com/WayScience/mitocheck_data) and used to create [training_data.csv.gz](../1.format_data/data/training_data.csv.gz).
+In this repository, all training data is downloaded from a version controlled [mitocheck_data](https://github.com/WayScience/mitocheck_data).
 
 The version of mitocheck_data used is specified by the hash corresponding to a current commit.
+The current hash being used is `19bfa5b0959d6b7536f83e7bb85745ba3edf7ff9` which corresponds to [mitocheck_data/19bfa5b](https://github.com/WayScience/mitocheck_data/tree/19bfa5b0959d6b7536f83e7bb85745ba3edf7ff9).
+The `hash` variable can be set in [download_data.ipynb](download_data.ipynb) to change which version of mitocheck_data is being accessed.
 
-The current hash being used is `de21b9c3201ba4298db2b1704f3ae510a5dc47e2` which corresponds to [mitocheck_data/de21b9c](https://github.com/WayScience/mitocheck_data/tree/de21b9c3201ba4298db2b1704f3ae510a5dc47e2).
+## Step 1: Download Data
 
-The `hash` variable can be set in [format_training_data.ipynb](../1.format_data/format_training_data.ipynb) to changed which version of mitocheck_data is being accessed.
+Use the commands below to download labeled training dataset:
+
+```sh
+# Make sure you are located in 0.download_data
+cd 0.download_data
+
+# Activate phenotypic_profiling conda environment
+conda activate phenotypic_profiling
+
+# Download data
+bash download_data.sh
+```