Unicycler is an assembly pipeline for bacterial genomes.
See versions which are available:
$ module avail unicycler
Load one version into your environment and run it:
$ module load unicycler/0.5.0 $ unicycler
#!/usr/bin/env bash
#SBATCH -p batch
#SBATCH -n 4
#SBATCH -J unicycler
module load unicycler/0.5.0
readonly DATADIR=~/sample_data
readonly OUTDIR=/var/scratch/2019-02-15-aorth-unicycler
# create output directory on compute node
mkdir -p ${OUTDIR}
# run unicycler with the number of threads allocated by SLURM
unicycler -t ${SLURM_NTASKS} -1 ${DATADIR}/short_reads_1.fastq.gz -2 ${DATADIR}/short_reads_2.fastq.gz -o ${OUTDIR}
echo
echo "Remember to check (and clean!) output directory on ${SLURM_JOB_NODELIST}:"
echo
echo " ${OUTDIR}"
By default Unicycler will use four CPU threads. Please make sure to set this parameter properly according to the SLURM job request.
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/rrwick/Unicycler/archive/refs/tags/v0.5.0.tar.gz $ tar xf v0.5.0.tar.gz $ cd Unicycler-0.5.0 $ module load python/3.8 $ sudo mkdir -p /export/apps/unicycler/0.5.0 $ sudo chown aorth /export/apps/unicycler/0.5.0 $ python3.8 setup.py install --prefix=/export/apps/unicycler/0.5.0 $ sudo chown -R root:root /export/apps/unicycler/0.5.0