GDC-client

Description

From the Genomic Data Commons (GDC) Home Page: The GDC Data Transfer Tool, a command-line driven application, provides an optimized method of transferring data to and from the GDC and enables resumption of interrupted transfers.

Version

  • 1.4.0

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Running GDC-client on CIRCE/SC

The GDC-client user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for GDC Data Transfer Tool, and execute the gdc-client binary:

[user@itn0 ~]$ srun --time=24:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/gdc-client/1.4.0
[user@wh-520-4-1 ~]$ gdc-client download -m gdc_manifest_6746fe840d924cf623b4634b5ec6c630bd4c06b5.txt


Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you want to download data using a manifest file, you would set up a submit script to use gdc-client like the following.

#!/bin/bash
#
#SBATCH --job-name=bamtools-test
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.bamtools-test

#### SLURM 1 processor gdc-client example to run for 24 hours.

# Load the gdc-client module:
module load apps/gdc-client/1.4.0

# Start gdc-client download
gdc-client download -m gdc_manifest_6746fe840d924cf623b4634b5ec6c630bd4c06b5.txt

 
Next, be sure that you are in the correct job directory, and run the sbatch command to submit the job:

[user@itn0 ~]$ cd my/jobdir
[user@itn0 jobdir]$ sbatch ./gdc-client-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with GDC-client to the IT Help Desk: rc-help@usf.edu