SMRTLINK-Teaching: Difference between revisions
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=== Version === | === Version === | ||
5.0. | 5.1.0.26412 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/gb/smrtlink/5.0. | 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 | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml smrtlink/5.0. | ml smrtlink/5.1.0.26412 | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml smrtlink/5.0. | ml smrtlink/5.1.0.26412<br> | ||
pbsmrtpipe <u>[options]</u><br> | pbsmrtpipe <u>[options]</u><br> | ||
</div> | </div> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml smrtlink/5.0. | ml smrtlink/5.1.0.26412 | ||
pbsmrtpipe -h | pbsmrtpipe -h | ||
{pipeline,pipeline-id,task,show-templates,show-template-details,show-tasks,show-task-details,show-workflow-options,run-diagnostic,show-chunk-operators} | |||
</pre> | </pre> | ||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
Revision as of 12:34, 13 August 2018
Category
Bioinformatics
Program On
Teaching
Version
5.1.0.26412
Author / Distributor
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
{pipeline,pipeline-id,task,show-templates,show-template-details,show-tasks,show-task-details,show-workflow-options,run-diagnostic,show-chunk-operators}
Installation
Source code is obtained from SMRTLINK
System
64-bit Linux