Merge pull request #52 from ncihtan/add-synapse-to-sbcgc-page

Add Synapse to CDS page

open_access/biq_query.md

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 # Google BigQuery

open_access/synapse_to_cds.md

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+
+---
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+---
+
+# Accessing HTAN open access dat stored in Synapse via SB-CGC
+
+HTAN’s open-access data, including most datasets, is hosted on Synapse and can be loaded into the SevenBridges Cancer Genomics Cloud using the following instructions. Note that open-access Level 2 images are available separately through the Cancer Data Service (CDS).
+
+## Video walkthrough
+
+[Watch video walkthrough on Zoom](https://us02web.zoom.us/clips/share/JNSyNG3rPRoWVYjWrYNiV-Z9Tv-TYIKdb54YLB6pk6CRhhnEQ0g14a4-2hItZXGOYXq3CzcSVjgNTL7HMhHjUm72.cd78QzhYRY4j02Mw)
+
+<div style="position: relative; width: 100%; height: 0; padding-bottom: 56.25%;">
+    <iframe src="https://us02web.zoom.us/clips/embed/JNSyNG3rPRoWVYjWrYNiV-Z9Tv-TYIKdb54YLB6pk6CRhhnEQ0g14a4-2hItZXGOYXq3CzcSVjgNTL7HMhHjUm72.cd78QzhYRY4j02Mw" 
+            frameborder="0" allowfullscreen="allowfullscreen" 
+            style="position: absolute; width: 100%; height: 100%; top: 0; left: 0;">
+    </iframe>
+</div>
+
+
+---
+
+## Step-by-Step Guide
+
+### 1. Start a Data Studio Instance
+1. Go to [CancerGenomicsCloud.org](https://cancergenomicscloud.org).
+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 [Synapse.org](https://synapse.org).
+   - 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 [HTAN Data Portal](https://data.humantumoratlas.org) 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
+
+- [SevenBridges CGC](https://cancergenomicscloud.org)
+- [Synapse](https://synapse.org)
+- [HTAN Data Portal](https://data.humantumoratlas.org)
+- [Synapse Python/CLI Client Documentation](https://python-docs.synapse.org)