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Bowtie
Bowtie is a sequencing toolset for aligning sets of DNA into large genomes.
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Workflow
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Installing Bowtie with Spack
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@chead1 (mycluster1) ~]$ flight env create spack- Activate the environment:
[flight@chead1 (mycluster1) ~]$ flight env activate spack- Install bowtie:
<spack> [flight@chead1 (mycluster1) ~]$ spack install bowtie
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Running a Bowtie Job
- Download example ecoli data:
<spack> [flight@chead1 (mycluster1) ~]$ flight silo file pull openflight:bowtie/ecoli.fq- 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- Submit the job to the queue:
<spack> [flight@chead1 (mycluster1) ~]$ sbatch ecoli-job.shThe results can then be reviewed from the slurm output file for the job in the current working directory.