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Bioinformatics - Trinity

Instructions on how to run (and, if needed, install a customized version of) Trinity

Trinity is a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

  1. Running Trinity on Thunder
  2. Install customized Tromoty on Thunder
Please refer to the CCAST User Guide and the the article Running Bioinformatics Software on HPC Clusters for general information about using CCAST resources and running bioinformatics software on CCAST's HPC clusters.

1. Running Trinity on Thunder


Example: Assemble transcriptomic sequences into artifacts


Location: /gpfs1/projects/ccastest/training/examples/Trinity_example


File list

· trinity_job.pbs: job submission script   

· reads.left.fq.gz: compressed paired-end sequences in fastq format

· reads.right.fq.gz: compressed paired-end sequences in fastq format


Steps

· Copy example directory to your SCRATCH directory

o    cp -r /gpfs1/projects/ccastest/training/examples/Trinity_example $SCRATCH

· Go to the copied directory

o    cd  $SCRATCH/Trinity_example

· Edit the job submission script as needed, then submit the job

o    qsub trinity_job.pbs


2. Install Customized Trinity on Thunder

Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.

Summary

(a) CMake 3.1 or higher is required for build; (available via “module load cmake”)

(b) SAMtools is required; (available via “module load SAMtools”)

(c) bowtie2 (available via “module load Bowtie2”)

(d) jellyfish  v2+ (install described below)

(e) salmon (install described below)  

(f) Support OpenMP.

Details

In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME is your username on Thunder.


(a) Load modules 

·       Load the CMake:

o    module load cmake

·       Load samtools:

o    module load SAMtools

·       Load bowtie2:

o    module load Bowtie2

(b) Install Jellyfish (Skip if using system Jellyfish): 

·       Go to software directory:

o    cd /gpfs1/home/USERNAME/SOFTWARE

·       Download:

o    wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-2.2.10.tar.gz

·       Unzip

o    tar -zxvf jellyfish-2.2.10.tar.gz

·       Go to unzipped directory:

o    cd jellyfish-2.2.10

·       Configure and specify where Jellyfish will be installed:

o    ./configure –prefix=/gpfs1/home/USERNAME/SOFTWARE/Jellyfish_install_here

·       Build

o    make

·       Install

o    make install

(c) Binary Install Salmon (Skip if using system Salmon):

·       Go to software directory:

o    cd /gpfs1/home/USERNAME/SOFTWARE

·       Directly download the binary: 

o    "wget https://github.com/COMBINE-lab/salmon/releases/download/v0.13.1/salmon-0.13.1_linux_x86_64.tar.gz

·       Unzip: 

o    "tar -zxvf salmon-0.13.1_linux_x86_64.tar.gz

(d) Install Trinity

·       Go to your software directory:

o    cd /gpfs1/home/USERNAME/SOFTWARE

·       Download Trinity from the author’s website:

o    wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.8.4.tar.gz

·       Unzip the downloaded file to the current location:

o    tar -zxvf Trinity-v2.8.4.tar.gz

·       Go to the trinityrnaseq-Trinity-v2.8.4 directory:

o    cd trinityrnaseq-Trinity-v2.8.4

·       Build:

o    make

·       Build plugins:

o    make plugins” 

(e) Test Trinity

·       Copy built-in-test directory: 

o    cd /gpfs1/scratch/USERNAME

o    cp -r /gpfs1/home/USERNAME/SOFTWARE/trinityrnaseq-Trinity-v2.8.4/sample_data/test_Trinity_Assembly .

o    cd test_Trinity_Assembly

·       Test example 1: Write and submit the job to run the build-in-test file "runMe.sh".

o    "qsub Trinity_buildin_job.pbs"

-------------------------------------Trinity_buildin_job.pbs--------------------------------------------

#!/bin/bash 
#PBS -q default 
#PBS -N trinity_self_test 
#PBS -l select=1:mem=10gb:ncpus=4 
#PBS -l walltime=02:00:00 
#PBS -W group_list=x-ccast-prj-[your project group name here]
## Only load modules for software for which you are not using your own installation
module load SAMtools
module load Bowtie2
cd $PBS_O_WORKDIR
#add software to path if not using system versions
export PATH=$PATH:/gpfs1/home/USERNAME/SOFTWARE/salmon-latest_linux_x86_64/bin
export PATH=$PATH:/gpfs1/home/USERNAME/SOFTWARE/Jellyfish_install_here/bin
export PATH=$PATH: /gpfs1/home/USERNAME/SOFTWARE/trinityrnaseq-Trinity-v2.8.4/bin
./runMe.sh
exit 0 

·       Test example 2: Write and submit a job to run a single command.

o    "qsub trinity_job.pbs"

-------------------------------------trinity_job.pbs--------------------------------------------

#!/bin/bash 
#PBS -q default 
#PBS -N trinity_test 
#PBS -l select=1:mem=10gb:ncpus=4 
#PBS -l walltime=02:00:00 
#PBS -W group_list=x-ccast-prj-[your project group name here]
 
module load SAMtools
module load Bowtie2
 
cd $PBS_O_WORKDIR
 
# Set path to Trinity root directory
export PATH=$PATH:/gpfs1/home/USERNAME/SOFTWARE/salmon-latest_linux_x86_64/bin
export PATH=$PATH:/gpfs1/home/USERNAME/SOFTWARE/Jellyfish_install_here/bin
export TRINITY_HOME=/gpfs1/home/USERNAME/SOFTWARE/trinityrnaseq-Trinity-v2.8.4/bin
 
${TRINITY_HOME}/Trinity --seqType fq --max_memory 10G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --output trinity_single_out_dir --CPU $NCPUS
 
exit 0 


See Also:




Keywords:ccast, hpc, thunder, bioinformatics, trinity, jellyfish, salmon   Doc ID:108087
Owner:Liu Y.Group:IT Knowledge Base
Created:2020-12-27 17:37 CDTUpdated:2020-12-29 02:08 CDT
Sites:IT Knowledge Base
CleanURL:https://kb.ndsu.edu/trinity
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