-- PanACoTA --

This README file provides some essential information to install/use PanACoTA. But it is better to read the full documentation, providing more details :

PanACoTA is a software providing tools for large scale comparative genomics:

• annotation of genomes
• pan-genome
• persistent genome
• phylogenetic tree from persistent genome

Installation

Dependencies

PanACoTA is written in python3. So, you need python3 (and pip3 for installation) to run it.

Its external dependencies are:

• prokka (to annotate the genomes)
• mmseqs (to generate pangenomes)
• mafft (to align persistent genome)
• At least one of those softwares, to infer a phylogenetic tree:
  • FastTreeMP: We advise to download C code, and compile as described here above.
  • FastME
  • Quicktree

To be able to install the dependencies, make sure you already have:

• tar
• git
• wget
• bioperl, java and some other base packages required for prokka: see Prokka README for more information.

For FastTree, we advise to download C code from here, and compile it using:

gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree-2.1.9.c -lm

You can then add the output FastTreeMP to your $PATH to be able to run it from everywhere.

Downloading and updating PanACoTA

You can download PanACoTA source code by downloading a zip file, or by cloning its gitlab repository. By cloning the gitlab repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:

git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation

Give your gitlab login, and password.

This will create a repository called pipeline_annotation. Go inside this repository to install PanACoTA, as described hereafter.

If a new version of PanACoTA is released, and you want to use it, type the following command to update the source code:

git pull

Then, you will be able to upgrade to the new version (see bellow).

Installing PanACoTA (final mode)

To install PanACoTA, and all its dependencies, from the root directory, type:

./make

or

./make install

You will then be able to use the package from any directory in your computer, just as any other software.

If you have permission issues, you can either use 'sudo' before the previous command lines to install it as root, or add the --user option to install it locally.

Warning: If you plan to work on the scripts, choose the development installation (see Development section).

Note: Dependencies installed by make:

• prokka
• barrnap (if prokka is not already installed)

Uninstalling PanACoTA

If you don't want PanACoTA anymore, or if you want to install a newer version, uninstall it by typing:

./make uninstall

Upgrade to new version

If you want to install a new version of PanACoTA (and you downloaded it by cloning the gitlab repository):

• update source code to the new version (git pull)
• upgrade installation to the new version (./make upgrade)

If you installed it by downloading a zip file, Uninstall it, and install the new version (by cloning gitlab repository, or downloading the new zip file).

Cleaning dependencies

If you installed the dependencies (such as prokka) via our installation script, but now want to install your own version, you can remove all dependencies downloaded and installed by make by doing:

./make clean

Running PanACoTA

Quick run

PanACoTA contains 5 different subcommands:

• annotate (annotate all genomes of the dataset, after a quality control)
• pangenome (generate pan-genome)
• corepers (generate core-genome or persistent-genome)
• align (align core/persistent families)
• tree (infer phylogenetic tree from persistent genome)

You can run them by typing:

PanACoTA <subcommand_name> <arguments_for_subcommand>

Each subcommand has its own options and inputs. To get the list of required arguments and other available options for the subcommand you want to run, type:

PanACoTA <subcommand> -h

Examples

We provide a folder, Examples, containing genomic sequences (in Examples/genomes) and examples of input files (in Examples/input_files) for the software. In the example part of documentation, you will find information explaining you how to run the different modules of PanACoTA with this dataset, so that you can try the software. We also describe the results that should be created by each command line.

Note: the provided genomic sequences are taken from real genomes, but then modified and shortened in order to have an example showing different situations, but running very fast. Hence, the examples results should not be interpreted biologically!

Documentation

You can find more information in PanACoTA documentation!

Development

This part is for people who want to work on developing PanACoTA package.

Installing PanACoTA (development mode)

If you want to install PanACoTA while still working on modifying the scripts, type:

./make develop

Your changes will then be taken into account. As you installed the package, you will be able to run it from any directory in your computer.

If you don't want to install the software, you can still test it, and contribute to the tests and documentation by installing the libraries needed for the software, and those needed for development by running:

pip3 install -r requirements.txt  # dependencies used by PanACoTA
pip3 install -r requirements-dev.txt  # libraries used to run tests, generate documentation etc.

Note: biopython is only used for 'tree' subcommand, with option --soft fastme or --soft quicktree. If you do not plan to use this, you do not need to install biopython. You can comment the biopython>=1.60 line in requirements.txt (add a # at the beginning of the line).

Running Tests

If you want to work on the scripts, you can use the tests provided with the software, used to check each of its functionalities. To run the tests, run, from the root of the project:

PYTHONPATH+=. py.test test/test_unit
PYTHONPATH+=. py.test test/test_functional

or, if you installed the package (final or development mode):

py.test test/test_unit
py.test test/test_functional

Add -sv for more details on each test.

Contributing to documentation

The full documentation, found here is generated with sphinx. You can add your contribution to it. To generate the html documentation locally, go to doc/sources directory, and run:

make html

Then, open doc/build/html/index.html on your browser.

The online version will be automatically updated when pushed on master branch.