GapFiller-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=GapFiller.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=GapFiller.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=GapFiller.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml GapFiller/2.1.1-foss-2016b | ml GapFiller/2.1.1-foss-2016b | ||
NA | |||
</pre> | </pre> | ||
Revision as of 14:03, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.1.1
Author / Distributor
Description
"GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data." More details are at GapFiller
Running Program
The last version of this application is at /usr/local/apps/eb/GapFiller/2.1.1-foss-2016b
To use this version, please load the module with
ml GapFiller/2.1.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_GapFiller
#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=GapFiller.%j.out
#SBATCH --error=GapFiller.%j.err
cd $SLURM_SUBMIT_DIR
ml GapFiller/2.1.1-foss-2016b
NA [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 GapFiller/2.1.1-foss-2016b NA
Installation
Source code is obtained from GapFiller
System
64-bit Linux