Bowtie2 short read mapper
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.
The runtime environment sets the following environment variables:
- BOWTIE_DIR points to the BOWTIE base directory
- PATH is set so that the $BOWTIE_DIR is included in the path
- BOWTIEDB is set to a suitable temporary directory for unpacking the datasets
- BOWTIE_NUM_CPUS is set to the number of allocated CPUs for this job. Remember to use bowtie2 -p BOWTIE_NUM_CPUS ... when running.
System administrator guide for installing the RE
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 firstname.lastname@example.org if you have any Bowtie pecific questions.