dbGaP download and decryption of GTEx data

Download and set up SRA Toolkit

wget -O ~/sratoolkit.current-centos_linux64 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz
tar xvf sratoolkit.current-centos_linux64.tar.gz

Ensure you have the repository key (*.ngc) downloaded to the server.

VDB Config

Run the vdb-config setup

./sratoolkit.current-centos_linux64/bin/vdb-config -i

This will start a curses GUI.

Recommended Settings

Make sure 1 and 2 are checked

4: Navigate to key. First, navigate to the directory, then hit tab and select the file.

5: If necessary, change the download directory (to /data, maybe)

After importing the key, you can change the repo directory.

This directory can be separate from the actual download directory, but the decrypt command is run from this one.

Download and set-up Aspera

wget http://download.asperasoft.com/download/sw/connect/3.6.2/aspera-connect-3.6.2.117442-linux-64.tar.gz
tar xvf aspera-connect-3.6.2.117442-linux-64.tar.gz
./aspera-connect-3.6.2.117442-linux-64.sh

This installs the binaries to ~/.aspera/connect/bin and the ssh keys to ~/.aspera/connect/etc.

Run ascp to download files

Copy the entire string from the email to a file and run the parse_dl_file.sh script.

echo "$string" > dl_string.txt

export $aspera_bin=/path/to/.aspera/connect/bin/ascp
export $aspera_key=/path/to/.aspera/connect/etc/asperaweb_id_dsa.openssh
sh parse_dl_file.sh dl_string.txt

This downloads the files to a directory in /data named after the download ID.

Descrypt the downloaded files

Navigate to the dbGaP project directory, not the downloaded files directory.

Run the vdb-decrypt script from the project directory, passing the location of the downloaded files.

/path/to/vdb-decrypt /data/$dl_id

This decrypts the files within the download directory.