# Accessing Synapse Open Access Data in SB-CGC

<a href="https://www.cancergenomicscloud.org/" target="_blank" rel="noopener noreferrer">Seven Bridges Cancer Genomics Cloud (SB-CGC)</a> is a cloud platform for the analysis and storage of large cancer datasets. 

HTAN’s open-access data, including most datasets, is hosted on Synapse and can be loaded into SB-CGC using the following instructions. Note that open-access Level 2 images are available separately through the National Cancer Institutes's [General Commons (GC)](cds_cgc.md).

## Video walkthrough

[Watch video walkthrough on Zoom](https://us02web.zoom.us/clips/share/JNSyNG3rPRoWVYjWrYNiV-Z9Tv-TYIKdb54YLB6pk6CRhhnEQ0g14a4-2hItZXGOYXq3CzcSVjgNTL7HMhHjUm72.cd78QzhYRY4j02Mw)

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            style="position: absolute; width: 100%; height: 100%; top: 0; left: 0;">
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## Step-by-Step Guide

### 1. Start a Data Studio Instance
1. Go to <a href="https://cancergenomicscloud.org" target="_blank" rel="noopener noreferrer">CancerGenomicsCloud.org</a>.
2. Log in and launch a Data Studio instance with JupyterLab.

### 2. Install and Configure Synapse Client
1. Open the Terminal in JupyterLab.
2. Install the Synapse client (if not already installed) by typing:
   ```bash
   pip install synapseclient
   ```
3. Obtain a Personal Access Token:
   - Log into <a href="https://synapse.org" target="_blank" rel="noopener noreferrer">Synapse.org</a>.
   - Go to Account Settings > Personal Access Tokens.
   - Create a new token with “View and Download” permissions and copy the token.
4. Configure Synapse client with the Token:
   - In the JupyterLab Terminal, type:
     ```bash
     synapse config
     ```
   - When prompted, enter your Synapse username (optional) and paste the token.

### 3. Select Files from the HTAN Data Portal
1. Visit the <a href="https://data.humantumoratlas.org/explore" target="_blank" rel="noopener noreferrer">HTAN Data Portal Explore Page</a>[]() and find the data files you need (e.g., single-cell RNA-seq data in H5AD format).
2. Click the purple “Download selected files” button for the chosen files.
3. Copy the download commands (e.g., `synapse get syn1234`).

### 4. Download Files into the Data Studio Instance
1. Paste the copied download commands into the JupyterLab Terminal.
2. Verify that the files are in the workspace directory. You can now use these files within notebooks in the Data Studio instance.

### 5. Move Files to Output Folder
- Move files to the `output-files` directory to ensure they sync with your CGC project:
  ```bash
  cp <filename> ../output-files
  ```

### 6. Stop Data Studio Instance
1. Stop the Data Studio instance to trigger synchronization.
2. Check your project files on CGC; the downloaded files should now be available for further use.

---

## Useful Links

- <a href="https://cancergenomicscloud.org" target="_blank" rel="noopener noreferrer">SevenBridges CGC</a>[]()
- <a href="https://synapse.org" target="_blank" rel="noopener noreferrer">Synapse</a>
- <a href="https://data.humantumoratlas.org" target="_blank" rel="noopener noreferrer">HTAN Data Portal</a>
- <a href="https://python-docs.synapse.org" target="_blank" rel="noopener noreferrer">Synapse Python/CLI Client Documentation</a>