Installation

Requirements

Phylociraptor extensively uses software containers and thus has only a minimum number of dependencies:

Linux or MacOS operating system
globally installed singularity 3.4.1+
installed snakemake 6.0.2+ (eg. in an anaconda environment)

On a HPC cluster (when utilizing parallel job execution):

SGE, SLURM or TORQUE job scheduling system

Obtaining phylocirator

Phylociraptor is available on GitHub. You can download it here .

The probably best way is to clone the repository directly using git (if available).

$ git clone --recursive https://github.com/reslp/phylociraptor.git
$ cd phylocirpator
$ ./phylociraptor
Welcome to phylociraptor, the rapid phylogenomic tree calculator

Usage: phylociraptor <command> <arguments>

Commands:
        setup                   Setup pipeline
        orthology               Infer orthologs in a set of genomes
        filter-orthology        Filter orthology results
        align                   Create alignments for orthologous genes
        filter-align            Trim and filter alignments
        model                   Perform modeltesting
        mltree                  Calculate Maximum-Likelihood phylogenomic trees
        speciestree             Calculate gene trees and species tree
        njtree                  Calculate Neighbor-Joining tree

        report                  Create a HTML report of the run
        check                   Quickly check status of the run

        -v, --version           Print version
        -h, --help              Display help

Example:
        To see options for the setup step:
        ./phylociraptor setup -h

        To run orthology inferrence for a set of genomes on a SLURM cluster:
        ./phylociraptor orthology -t slurm -c data/cluster-config-SLURM.yaml

        To filter alignments overwriting the number of parsimony informative sites set in the config file:
        ./phylciraptor filter-align --npars_cutoff 12

phylociraptor: error: the following arguments are required: command, arguments

Note

If you don’t have git available, you can also download phylociraptor directly as ZIP file and unpack it to the desired location.

Create a conda environment for snakemake

Warning

It is recommended to install snakemake using conda into it’s own environment. Other options, such as loading snakemake as environment module can sometimes cause problems (eg. on HPC systems)

If you don’t have conda installed, first look here .

$ conda install -n base -c conda-forge mamba
$ mamba create -c conda-forge -c bioconda -n snakemake snakemake=6.0.2
$ conda activate snakemake

When you run phylociraptor this environment needs to be activated.

Additional information on how to install snakemake can be found here .

Optional: Customize cluster configuration settings to fit your HPC environment

phylociraptor will automatically submit jobs to SLURM, SGE and TORQUE job submission systems using sbatch or qsub.

For this to work you will probably need to edit the correct cluster configuration file.

The files are data/cluster-config-SLURM.yaml.template and data/cluster-config-SGE.yaml.template.