SMRTLINK-Teaching

Category

Bioinformatics

Program On

Teaching

Version

5.0.1.9585

Author / Distributor

SMRTLINK

Description

"PacBio open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided." More details are at SMRTLINK

Running Program

The last version of this application is at /usr/local/apps/gb/smrtlink/5.0.1.9585

To use this version, please load the module with

ml smrtlink/5.0.1.9585 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_SMRTLINK
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SMRTLINK.%j.out
#SBATCH --error=SMRTLINK.%j.err

cd $SLURM_SUBMIT_DIR
ml smrtlink/5.0.1.9585
pbsmrtpipe [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

SMRTLINK

ml smrtlink/5.0.1.9585 
pbsmrtpipe  -h

usage: pbsmrtpipe [-h] [--version]
                  {pipeline,pipeline-id,task,show-templates,show-template-details,show-tasks,show-task-details,show-workflow-options,run-diagnostic,show-chunk-operators}
 

Back to Top

Installation

Source code is obtained from SMRTLINK

System

64-bit Linux