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pipeline_annotation

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  • -- genomeAPCAT --

    build status coverage report

    genome APCAT is a software providing tools for large scale comparative genomics:

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

    Installation

    Dependencies

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

    Its external dependencies are:

    • prokka (to annotate the genomes). If you do not already have it, this software will be automatically installed by make script, along with genomeAPCAT (see Install section )
    • mmseqs (to generate pangenomes)
    • fftns (from mafft, to align persistent genome)
    • At least one of those softwares, to infer a phylogenetic tree:

    You can either install the external dependencies yourself, with the version you want, or use the installation script make, which will install the dependencies.

    To be able to install the dependencies (by yourself, or with the installation script), 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 -lm FastTree-2.1.9.c

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

    Downloading and updating genomeAPCAT

    You can download genomeAPCAT source code by downloading an archive (zip, tar.gz), 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 genomeAPCAT, as described hereafter.

    If a new version of genomeAPCAT 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 genomeAPCAT (final mode)

    To install genomeAPCAT, 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 genomeAPCAT

    If you don't want genomeAPCAT 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 genomeAPCAT:

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

    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 genomeAPCAT

    Quick run

    genomeAPCAT 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:

    genomeAPCAT <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:

    genomeAPCAT <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 this folder, you will also find a README file, explaining you how to run the different modules of genomeAPCAT 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

    Not done yet, there will be a documentation describing each module and its arguments/options...

    Development

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

    Installing genomeAPCAT (development mode)

    If you want to install genomeAPCAT 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.

    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