Getting Started

Docker, Singularity

You can avoid all the installation and setup process by loading Phigaro in a prebuilt container. Now, Phigaro is available in Docker and Singularity! You can find Dockerfile and Singularity files for creating images at this repository. Some useful paths in containers:

phigaro: /root/miniconda3/bin/phigaro
config.yml: /root/.phigaro/config.yml
test_data: /test_data

---

Requirements

• Python: Python 3+.
  Python 2.7 is available, but it is no longer supported.

  • pip utility is also required (sudo apt-get install python-pip on Ubuntu).

• Prodigal: Download it from https://github.com/hyattpd/Prodigal/wiki/installation and follow the instructions.

• HMMER: Download it from http://hmmer.org/

• locate: In order to setup Phigaro easier, you need locate.

  • It is present in the latest Ubuntu distributions, but in case you don't have it, install it with sudo apt-get install locate.
  • For MacOS, you may need to add the following softlink ln -s /usr/libexec/locate.updatedb /usr/local/bin/updated and run brew install wget.

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Installation

Via bioconda

conda install -c bioconda phigaro

Via pip

pip3 install phigaro --user

Via conda

conda env create -f environment.yml
conda activate phigaro_env

Where environment.yml can be downloaded form this repository or created manually:

name: phigaro_env
dependencies:
  - python=3.7
  - pip
  - bioconda::prodigal
  - bioconda::hmmer
  - pip:
    - phigaro

---

Setup

Create a config file with:

phigaro-setup

It may take some time, since you are downloading the databases.

Rootless Mode

By default, root permissions are required for the installation. But you can disable it by adding a flag to phigaro-setup:

phigaro-setup --no-updatedb

Allpvoghmms Download Problem

If for some reason the downloading of pVOG database failed, you can download these files manually from our server or Google Drive. You should store the files at the directory $HOME/.phigaro/pvog.

Manual Setup

Also, you can manually create/change a config.yml file and write the hmmer, prodigal and pvogs paths like it is done in an example below. Other parameters should stay the same for the proper work of Phigaro unless you want to change them on purpose. A config.yml file should be placed to $HOME/.phigaro folder or you can provide the path to the config file every time you run phigaro with the -c or --config parameter.

For the pvogs you should download all the files to the pvog (or any other folder) via the link or from Google Drive if it wasn't done previously by phigaro-setup.

The content of the config.yml file could be found in the repository or can be copied from down here. It is possible that you may need to change the following paths:

• hmmer: bin
• hmmer: pvog_path
• prodigal: bin

hmmer:
  bin: /usr/local/bin/hmmsearch
  e_value_threshold: 0.00445
  pvog_path: /root/.phigaro/pvog/allpvoghmms
phigaro:
  mean_gc: 0.46354823199323625
  penalty_black: 2.2
  penalty_white: 0.7
  threshold_max_abs: 52.96
  threshold_max_basic: 46.0
  threshold_max_without_gc: 11.42
  threshold_min_abs: 50.32
  threshold_min_basic: 45.39
  threshold_min_without_gc: 11.28
  window_len: 32
prodigal:
  bin: /root/miniconda3/bin/prodigal

All Options

Moreover, you may want to change a path of a config installation file or reconfigurate your Phigaro by adding special flags:

phigaro-setup --help
usage: phigaro-setup [-h] [-c CONFIG] [-p PVOG] [-f] [--no-updatedb]

Phigaro setup helper

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Path to a config.yml, default is
                        /home/polly/.phigaro/config.yml (default:
                        /home/polly/.phigaro/config.yml)
  -p PVOG, --pvog PVOG  pvogs directory, default is /home/polly/.phigaro/pvog
                        (default: /home/polly/.phigaro/pvog)
  -f, --force           Force configuration and rewrite config.yml if exists
                        (default: False)
  --no-updatedb         Do not run sudo updatedb (default: False)