From e407bae7e7ee357b4d182ca27d898c3e4e329739 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Fri, 1 Nov 2024 14:27:05 +0000 Subject: [PATCH 1/2] Add gen3 instructions --- open_access/cds_gen3.md | 77 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 open_access/cds_gen3.md diff --git a/open_access/cds_gen3.md b/open_access/cds_gen3.md new file mode 100644 index 00000000..6eb7c83b --- /dev/null +++ b/open_access/cds_gen3.md @@ -0,0 +1,77 @@ +--- +order: 993 +--- + +HTAN files avaliable througn the NCI CRDC Cancer Data Service can be downloaded in the terminal using the gen3 commend line client. + +## Video walkthrough + +
+ +## Step-by-step guide + + + +### Step 1: Set Up Your Environment + +- Open your terminal and create a clean Conda environment (or environment of your choice) with Python 3.11. +*Note: Python 3.12 is not compatible with the current version of the Gen3 client.* + + ``` + conda create -n gen3_env python=3.11 + conda activate gen3_env + ``` + +- Install the Gen3 client by running: + + ``` + pip install gen3 + ``` + +3. Verify the Gen3 client installation: + + ``` + gen3 --help + ``` +If help options are displayed, the installation was successful. + +### Step 2: Obtain and Configure API Credentials + +- Log in to the NCI Commons Framework at [nci-crdc.datacommons.io](https://nci-crdc.datacommons.io). +- Go to your profile settings, create a new API key, and download the credentials.json file. +- In the terminal, create the `.gen3` directory in your home folder if it doesn’t alreadyexist:- + ``` + mkdir ~/.gen3 + ``` + +- Move the credentials.json file to the `~/.gen3/` directory: + + ``` + mv path/to/credentials.json ~/.gen3/credentials.json + ``` + + +### Step 3: Select Files from the HTAN Data Portal + +- Go to the HTAN Data Portal and filter the files based on your criteria (e.g., open access CDS files). +- Select the files you want to download + +### Step 4: Use the Gen3 Client to Download Files + +- Select the "Download files" link and view the the gen client command for your selected files. +- Copy the Gen3 command and run it in your terminal. The command should look like this: + + ``` + gen3-client download-multiple --profile=nci-crdc --object-ids + ``` + +- **Run the command.** This may take a moment. You might see a warning initially, which is typically harmless and does not impact the download process. +- **Verify the Download.** Once the download completes, you should see the files in your directory. You’ll also receive a report showing successful downloads and any failed attempts (if any). For example: + ``` + (gen3) ataylor@ajt-mbp gen3-test % gen3 --endpoint=nci-crdc.datacommons.io/ drs-pull objects dg.4DFC/6221caa8-7e68-11ee-a468-172bb8261521 dg.4DFC/621d8a38-7e68-11ee-82bd-ef84a2cd1f8d + [2024-11-01 13:52:21,391][WARNING] Unable to process WTS response. Likely no WTS service running on this commons. Certain commands might fail. + {"succeeded": ["dg.4DFC/6221caa8-7e68-11ee-a468-172bb8261521", "dg.4DFC/621d8a38-7e68-11ee-82bd-ef84a2cd1f8d"], "failed": []} + + (gen3) ataylor@ajt-mbp gen3-test % ls + MIBITIFF_MBC_Point17_combined.ome.tiff MIBITIFF_MBC_Point21_combined.ome.tiff + ``` \ No newline at end of file From 2c864930f7e719899bf052881f7b0da3b1b96c79 Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Fri, 1 Nov 2024 14:27:21 +0000 Subject: [PATCH 2/2] Change BQ page order --- open_access/biq_query.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/open_access/biq_query.md b/open_access/biq_query.md index dcc29a7e..6586501f 100644 --- a/open_access/biq_query.md +++ b/open_access/biq_query.md @@ -1,5 +1,5 @@ --- -order: 993 +order: 992 --- # Google BigQuery