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Bowtie Workflow Example

Bowtie is a sequencing tool-set 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.

  1. Create a spack software environment: 
    [flight@chead1 (mycluster1) ~]$ flight env create spack
  2. Activate the environment: 
    [flight@chead1 (mycluster1) ~]$ flight env activate spack
  3. Install bowtie: 
    <spack> [flight@chead1 (mycluster1) ~]$ spack install bowtie

Running a Bowtie Job

  1. Download example ecoli data: 
    <spack> [flight@chead1 (mycluster1) ~]$ flight silo file pull openflight:bowtie/ecoli.fq
  2. Download an example job script to run in the current working directory: 
    <spack> [flight@chead1 (mycluster1) ~]$ flight silo file pull openflight:bowtie/ecoli-job.sh
  3. Submit the job to the queue: 
    <spack> [flight@chead1 (mycluster1) ~]$ sbatch ecoli-job.sh

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