# Bowtie

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

# Workflow

# 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

# Running a Bowtie Job

Download example ecoli data:

<spack> [flight@chead1 (mycluster1) ~]$ wget -O ecoli.fq http://tiny.cc/ecoli

Create a job script in the current working directory:

<spack> [flight@chead1 (mycluster1) ~]$ 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@chead1 (mycluster1) ~]$ sbatch mybowtiejob.sh

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