Lazypipe is a stand-alone pipeline for identifying viruses in host-associated or environmental samples. The main emphasis is on assembling, taxonomic binning and taxonomic profiling of bacterial/viral sequences.
Free to use and open source under MIT License.
All components of Lazypipe pipeline are available in Puhti. The Lazypipe home page provides detailed instruction how to set up your own Lazypipe environment to Puhti, but this is not needed if you use the Lazypipe module that is loaded with commands:
module load r-env-singularity module load biokit module load lazypipe
cp /appl/soft/bio/lazypipe/2.1/lazypipe/config.yaml config.yaml echo tmpdir: \"$(pwd)\" >> config.yaml lazypipe.pl
Normally you need to use the lazypipe.pl command only for testing. For real analysis tasks lazypipe module includes
sbatch-lazypipe command that you can use instead.
sbatch-lazypipe is a help tool that automatically generates a configuration file and a batch job file for a Lazypipe run and submits the job to batch job system of Puhti. The command uses the same command line options as the lazypipe.pl command. In addition sbatch-lazypipe asks user to define batch job resources (account, run time, memory, number of cores).
For example to execute the Example 1 from the Lazypipe home page, you would first need to download the reads and reference genome to your scratch directory in Puhti (in real cases you will get these input files from your own sources):
mkdir /scratch/my_project/data mkdir /scratch/my_project/genomes_host cd /scratch/my_project/data/ wget https://bitbucket.org/plyusnin/lazypipe/downloads/M15.tar.gz tar -xzvf M15.tar.gz cd /scratch/my_project/genomes_host wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/108/605/GCA_900108605.1_NNQGG.v01/GCA_900108605.1_NNQGG.v01_genomic.fna.gz
cd /scratch/my_project module load r-env-singularity module load biokit module load lazypipe sbatch-lazypipe -1 data/M15/M15_R1.fastq -S M15 -p main \ --hostgen genomes_host/GCA_900108605.1_NNQGG.v01_genomic.fna.gz
- accounting project
- maximum duration of the job (default 24 hours )
- memory reservation ( default 32G)
- number of computing cores to use ( default 8 )
- email notifications
After that your Lazypipe task is submitted to the batch job system for execution.