Trinity

Description

From the Trinity web site: Trinity assembles transcript sequences from Illumina RNA-Seq data.

Version

2.6.5

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

Trinity requires the following module file to run:

apps/trinity/2.6.5

See Modules for more information.

Running Trinity on CIRCE/SC

The Trinity 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.

How to Submit Jobs

Provided are directions for running an interactive job and a batch script for running Trinity as a multi-processor job. These scripts are provided as examples only.

Using the GUI Tools

Establishing a GUI connection to CIRCE/SC

To use Trinity, you will need to connect to CIRCE/SC with GUI redirection, either using:

CIRCE/SC Desktop Environment
SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
  - ```
  [user@localhost ~]$ ssh -X circe.rc.usf.edu
```
  or
- ```
[user@localhost ~]$ ssh -X sc.rc.usf.edu
```

Once connected to CIRCE, you can open Trinity using the steps below :

[user@login0 ~]$ srun --time=10:00:00 --nodes=1 --cpus-per-task=4 --pty /bin/bash
[user@wh-520-4-1 ~]$ module add apps/trinity/2.6.5
[user@wh-520-4-1 ~]$ Trinity -seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G

Distributed Parallel

This script (for this example, call it "trinity-test.sh") can be copied into your job directory (the folder with your input files and database files) and modified so that you can submit batch processes to the queues.

#!/bin/bash

#SBATCH --job-name=trinity-test
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --mem=20G


module add apps/trinity/2.6.5

Trinity --seqType fq --left left_input.fq --right right_input.fq --CPU $SLURM_NTASKS --max_memory 20G

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 ./trinity-test.sh

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

Documentation

Home Page, User Guides, and Manuals

Trinity Home Page:
- https://github.com/trinityrnaseq/trinityrnaseq/wiki
Trinity Documentation:
- https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity

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

Trinity Examples
- /apps/trinity/2.6.5/sample_data/test_Trinity_Assembly
- /apps/trinity/2.6.5/trinity_ext_sample_data

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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