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Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
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sjspielman and jashapiro committed Jul 11, 2024
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All examples below assume you are running the script from the root of the repository.

!!! tip "Log into AWS CLI before running the script"
Before running this script locally (i.e., not from an [ALSF-provided virtual computer](../../aws/index.md#lightsail-for-research-virtual-computing-with-aws)), you will need to be [logged into your AWS CLI profile](../../technical-setup/environment-setup/configure-aws-cli.md#logging-in-to-a-new-session).
Before running this script locally (i.e., not using [Lightsail for Research](../../aws/index.md#lightsail-for-research-virtual-computing-with-aws)), you will need to be [logged into your AWS CLI profile](../../technical-setup/environment-setup/configure-aws-cli.md#logging-in-to-a-new-session).
To do this, run the following commands in terminal before running the `download-results.py` script, and follow instructions to log in.

```sh
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## Accessing data from the ScPCA Portal

If you have not yet been [granted access to ScPCA data via AWS](./index.md#getting-access-to-aws), you will need to obtain data directly from [the ScPCA Portal that the Data Lab maintains](https://scpca.alexslemonade.org).
If you have not yet been [granted access to OpenScPCA AWS resources](./index.md#getting-access-to-aws), you will need to obtain data directly from [the ScPCA Portal](https://scpca.alexslemonade.org).
You can download the project(s) or sample(s) you are interested in analyzing from the ScPCA Portal.

Note that you can also access the [OpenScPCA test data](#accessing-test-data) before getting AWS access as well.
Note that you can download the [OpenScPCA test data](#accessing-test-data) before getting AWS access as well.


### Organizing data files
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You can then develop your analysis specifying the `data/current` path when reading in data.
This way, your directory names will be compatible with the file structure established by the [OpenScPCA data download script](#using-the-download-data-script).

Within `data/portal-downloads`, we further recommend organizing your files in the same manner [as the official OpenScPCA data download script does](#downloaded-data-file-structure), as in:
Within `data/portal-downloads`, we further recommend organizing your files in the same manner [as the OpenScPCA data download script does](#downloaded-data-file-structure), as in:

```sh
data
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