Bismark-Teaching
Category
Bioinformatics
Program On
Teaching
Version
0.22.1
Author / Distributor
Felix Krueger, Bioinformatics Group at the Babraham Institute
Description
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states. For more information, please see Babraham Institute
Running Program
- Version 0.22.1, installed at /usr/local/apps/eb/Bismark/0.22.1-foss-2016b
To use this version of Bismark, please first load the module with
module load Bismark/0.22.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=jobName
#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=Bismark.%j.out
#SBATCH --error=Bismark.%j.err
cd $SLURM_SUBMIT_DIR
module load Bismark/0.22.1-foss-2016b
bismark --parallel 4 [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
Installation
Binary code downloaded from Bismark
System
64-bit Linux