SMRTLINK-Teaching: Difference between revisions

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=== Version ===
=== Version ===
5.0.1.9585
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/5.0.1.9585
The last version of this application is at /usr/local/apps/gb/smrtlink/5.1.0.26412


To use this version, please loads the module with
To use this version, please load the module with
<pre class="gscript">
<pre class="gscript">
ml smrtlink/5.0.1.9585
ml smrtlink/5.1.0.26412
</pre>  
</pre>  


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


<div class="gscript2">
<div class="gscript2">
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cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml smrtlink/5.0.1.9585<br>     
ml smrtlink/5.1.0.26412<br>     
pbsmrtpipe  <u>[options]</u><br>   
pbsmrtpipe  <u>[options]</u><br>   
</div>
</div>
Line 58: Line 58:
   
   
<pre  class="gcommand">
<pre  class="gcommand">
ml smrtlink/5.0.1.9585
ml smrtlink/5.1.0.26412
pbsmrtpipe  pbsmrtpipe  -h
pbsmrtpipe  pbsmrtpipe  -h
[https://www.pacb.com/support/software-downloads SMRTLINK]
[https://www.pacb.com/support/software-downloads SMRTLINK]

Revision as of 12:40, 10 August 2018

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

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  pbsmrtpipe  -h
[https://www.pacb.com/support/software-downloads SMRTLINK]

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Installation

Source code is obtained from SMRTLINK

System

64-bit Linux