Description

From the TraCeR home page: TraCeR is a tool that reconstructs the sequences of rearranged and expressed T cell receptor genes from single-cell RNA-seq data. It then uses the TCR sequences to identify cells that have the same receptor sequences and so derive from the same original clonally-expanded cell.

Version

• 0.15.2

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

TraCeR requires the following module file to run:

• apps/tracer/0.15.2

• See Modules for more information.

Running TraCeR on CIRCE/SC

The TraCeR 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.

Submitting a Job

Use a submit script like the following to run TraCeR:

#!/bin/bash
#
#SBATCH --job-name=tracer-test
#SBATCH --nodes=1
#SBATCH --ntasks=8
#SBATCH --mem-per-cpu=1024
#SBATCH --output=output.%j.tracer-test
#SBATCH --time=01:00:00

#### SLURM single node tracer test 
#### to run for 1 hour 
#### using 8 processor cores and 8 GB of memory

module purge
module add apps/tracer/0.15.2

tracer test -p 8 -c /apps/tracer/0.15.2/tracer.conf -o tracer-test.out

 

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./tracer-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

• TraCeR Home Page
  • https://github.com/Teichlab/tracer
• TraCeR User's Guide
  • https://github.com/Teichlab/tracer/blob/master/README.md
  • /apps/tracer/0.15.2/README.md

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

• TraCeR Examples
  • /apps/tracer/0.15.2/test_data
• Configuration file needed for running TraCeR
  • /apps/tracer/0.15.2/tracer.conf

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

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