TIGRLab/external-dbgap

Name: external-dbgap

Owner: Kimel Family Translational Imaging-Genetics Research Lab

Description: null

Created: 2015-07-05 02:19:04.0

Updated: 2015-07-05 02:31:47.0

Pushed: 2015-07-05 20:32:44.0

Homepage: null

Size: 132

Language: null

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README

A project for organizing our dbGAP data

Datasets
instructions for decrypting dbGaP data

  1. Download latest version of decrypt tools. As of Jan 9 2015, the version is 2.4.3 (download file = decryption.2.4.3-ubuntu64.tar.gz)

  2. Untar:

    tar -xvf decryption.2.4.3-ubuntu64.tar.gz

  3. Run sratoolkit.jar, found within decryption.2.4.3-ubuntu64/bin:

    java -jar decryption.2.4.3-ubuntu64/bin/sratoolkit.jar

  4. In the dialogue box that appears, enter a directory path ending with ncbi/public. You will be asked if this directory should be created, click yes.

  5. Once the “workspace” has been created, select new from the dropdown menu and select “import repository”. Browse to find the .ngc file that you download from the NIH/dbGaP “Downloads” page for that particular dataset. The .ngc file (the “repository key”) is the same for each dataset downaloaded as part of the same dbGaP project number (i.e. 3457).

  6. Quit the SRA toolit setup GUI

  7. The toolkit setup GUI will have created a file in your home directory (even if you did not specify it as your desired respository location) called ~/.ncbi (hidden). Inside there should be two files, one called dbGaP-3457.enc_key (the number 3457 here is just an example of a dbGaP project number - this file, created automatically by the SRA toolkit setup GUI, should automatically have the correct project number in its name, as it is generated based on the imported repository key that includes this information), and one called user_settings.mkfg.

  8. The dbGaP-3457.enc_key file will have the NIH login password in it. It may be out of date, as this password will be whichever was used to create the dbGaP project request in the first place (i.e. when the project, not the request for any specific dataset within it, was initiated).

  9. From anywhere, run the vdb-passwd command within decryption.2.4.3-ubuntu64/bin. You will be prompted to enter a password; enter the original dbGaP password (i.e. the one in the dbGaP-3457.enc_key file). You will be prompted to re-enter the password; re-enter the same original password. You may encounter a warning saying that a folder (e.g. ~/Downloads) has excessive permissions. Ignore this warning.

  10. From the directory containing the ncbi folder (that was created in the first part of step 4), run the vdb-decrypt command found in decryption.2.4.3-ubuntu64/bin, with the top-level folder of the dowloaded data (should be a 5-digit number; 41904 is the example below) as the single input.

    decryption.2.4.3-ubuntu64/bin/vdb-decrypt /some_dir/dataset1/41904

  11. Throw a pinch of salt over your left shoulder, tap your desk, and cross your fingers.

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.