SAMtools-Teaching

From Research Computing Center Wiki
Revision as of 13:47, 10 August 2018 by Yhuang (talk | contribs)
Jump to navigation Jump to search

Category

Bioinformatics

Program On

Teaching

Version

0.1.19

Author / Distributor

SAMtools

Description

"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." More details are at SAMtools

Running Program

The last version of this application is at /usr/local/apps/eb/SAMtools/0.1.19-foss-2016b

To use this version, please load the module with

ml SAMtools/0.1.19-foss-2016b 

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

#!/bin/bash
#SBATCH --job-name=j_SAMtools
#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=SAMtools.%j.out

cd $SLURM_SUBMIT_DIR
ml SAMtools/0.1.19-foss-2016b
samtools [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 SAMtools/0.1.19-foss-2016b 
samtools samtools --help
[main] unrecognized command '--help'

Back to Top

Installation

Source code is obtained from SAMtools

System

64-bit Linux