SMRTLINK-Teaching

Category

Bioinformatics

Program On

Teaching

Version

5.1.0.26412

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/5.1.0.26412

To use this version, please load the module with

ml smrtlink/5.1.0.26412 

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/5.1.0.26412
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

ml smrtlink/5.1.0.26412 
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}
                  ...

Pbsmrtpipe workflow engine

positional arguments:
  {pipeline,pipeline-id,task,show-templates,show-template-details,show-tasks,show-task-details,show-workflow-options,run-diagnostic,show-chunk-operators}
                        commands
    pipeline            Run a pipeline using a pipeline template or with
                        explict Bindings and EntryPoints.
    pipeline-id         Run a registered pipeline by specifying the pipeline
                        id.
    task                Run Task (i.e., ToolContract) by id
    show-templates      List all pipeline templates. A pipeline 'id' can be
                        referenced in your my_pipeline.xml file using
                        '<import-template
                        id="pbsmrtpipe.pipelines.my_pipeline_id" />. This can
                        replace the explicit listing of EntryPoints and
                        Bindings.
    show-template-details
                        Show details about a specific Pipeline template.
    show-tasks          Show completed list of Tasks by id. Use ENV
                        PB_TOOL_CONTRACT_DIR to define a custom directory of
                        tool contracts. These TCs will override the installed
                        TCs (e.g., PB_TOOL_CONTRACT_DIR=/path/to/my-tc-dir/)
    show-task-details   Show Details of a particular task by id (e.g.,
                        'pbsmrtpipe.tasks.filter_report'). Use 'show-tasks' to
                        get a completed list of registered tasks.
    show-workflow-options
                        Display all workflow level options that can be set in
                        <options /> for preset.xml
    run-diagnostic      Diagnostic tests of preset.xml and cluster
                        configuration
    show-chunk-operators
                        Show a list of loaded chunk operators for
                        Scatter/Gather Tasks. Extend resource loading by
                        exporting ENV var PB_CHUNK_OPERATOR_DIR. Example
                        export PB_CHUNK_OPERATOR_DIR=/path/to/chunk-operators-
                        xml-dir

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

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Installation

Source code is obtained from SMRTLINK

System

64-bit Linux