unicycler-software
Table of Contents
Unicycler
Unicycler is an assembly pipeline for bacterial genomes.
Information
- Version: 0.47.0
- Added: February, 2019
Usage
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
Example Batch Job
#!/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.
Installation
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 $PATH
.
unicycler-software.txt · Last modified: 2020/01/21 09:38 by jean-baka