Name

APPS/BIO/BOWTIE-2.2.3

Description

Bowtie2 short read mapper

Status

Production

Last update

2014-09-22

Usage example

Here is a simple test case for the runtime environment.

Download the example job here.

The job description file bowtie2.xrsl:

&
(executable=run_bowtie2.sh)
(jobname=bowtie2)
(stdout=std.out)
(stderr=std.err)
(gmlog=gridlog)
(cputime=60)
(memory=4000)
(runtimeenvironment=APPS/BIO/BOWTIE-2.2.3)
(inputfiles= 
  ("chr_18.fa" "chr_18.fa")
  ("reads100k.fq" "reads100k.fq")
)
(outputfiles=
  ("output.sam" "output.sam")
)

Corresponding execution script run_bowtie.sh

#!/bin/sh

echo "Hello Bowtie2"
bowtie2-build -p $BOWTIE_NUM_CPUS chr_18.fa chr_18
bowtie2 -p $BOWTIE_NUM_CPUS chr_18 reads100k.fq > output.sam
exitcode=$?
echo "Bye Bowtie2!"
exit $exitcode

Here the actual run consists of two steps: 1. Indexing the reference genome (bowtie-build), 2. Running the mapping task (bowtie),  The exitcode from bowtie is used as the exit code for the script, this way ARC knows whether the job has succeeded or failed.

Interface definition

The runtime environment sets the following environment variables:

System administrator guide for installing the RE

Bowtie2 executables

Pre-compiled Bowtie2 executables can be downloaded from the Bowtie home page

wget http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip
unzip bowtie2-2.0.5-linux-x86_64.zip

Sample runtime environment for SLURM.

Modify the scripts as needed and save the main script in your ARC runtime directory as APPS/BIO/BOWTIE-2.0.0.

Contact information

Contact helpdesk@csc.fi if you have any Bowtie pecific questions.