Unicycler is an assembly pipeline for bacterial genomes.

• Version: 0.47.0
• Added: February, 2019
• Link: https://github.com/rrwick/Unicycler

See versions of unicycler which are available:

$ module avail unicycler

Load one version into your environment and run it:

$ module load unicycler/0.47.0
$ unicycler

#!/usr/bin/env bash
#SBATCH -p batch
#SBATCH -n 4
#SBATCH -J unicycler

module load unicycler/0.4.7

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/v0.4.7.zip
$ unzip v0.4.7.zip
$ cd Unicycler-0.4.7
$ sudo yum install centos-release-scl
$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 python36 python36-setuptools
$ scl enable devtoolset-6 bash
$ sudo mkdir -p /export/apps/unicycler/0.4.7
$ sudo chown aorth /export/apps/unicycler/0.4.7
$ python36 setup.py install --prefix=/export/apps/unicycler/0.4.7
$ sudo chown -R root:root /export/apps/unicycler/0.4.7

The devtoolset is used because Unicycler requires a GCC compiler newer than 4.9.1.

Note by JB: way after this install, on 21 Jan 2020, I had to change the header in /export/apps/unicycler/0.4.7/bin/unicycler from $ #!/usr/bin/python36 to $ #!/usr/bin/python3.6 because there is no (no longer?) python36 in the $PATH.