Bowtie

About

Bowtie is a sequencing toolset for aligning sets of DNA into large genomes.

Workflow

Installing Bowtie with Spack

Note

The flight environment will need to be activated before the environments can be created so be sure to run flight start or setup your environment to automatically activate the flight environment.

• Create a spack software environment:

  [flight@gateway1 (scooby) ~]$ flight env create spack
  

• Activate the environment:

  [flight@gateway1 (scooby) ~]$ flight env activate spack
  

• Install bowtie:

  <spack> [flight@gateway1 (scooby) ~]$ spack install bowtie
  

Running a Bowtie Job

• Download example ecoli data:

  <spack> [flight@gateway1 (scooby) ~]$ wget -O ecoli.fq http://tiny.cc/ecoli
  

• Create a job script in the current working directory:

  <spack> [flight@gateway1 (scooby) ~]$ cat << EOF > mybowtiejob.sh
  #!/bin/bash -l
  #SBATCH -N 1
  flight env activate spack
  spack load bowtie
  bowtie-build ecoli.fq e_coli
  EOF
  

• Submit the job to the queue:

  <spack> [flight@gateway1 (scooby) ~]$ sbatch mybowtiejob.sh
  

The results can then be reviewed from the slurm output file for the job in the current working directory.