README.rst

.. image::      docs/source/_images/frangiPANe.png


FrangiPANe
    a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.
Previously developed as a modular and interactive application based on Jupyter Book [1]_ , it has now been recoded and integrated into a Snakemake pipeline.


I - Installing FrangiPANe
#################

1.1 - Install the frangiPANe python package
=================

Requirement
-----------------

- `Git <https://git-scm.com/>`_

- `Singularity <https://...>`_


Clone the git repository
-----------------


::

   git clone https://forge.ird.fr/diade/frangipane.git

::

    cd PATH_2_FRANGIPANE_DIRECTORY
    python3 -m pip install -U pip setuptools build
    python3 -m pip install -e .


.. code-block:: rst

    NOTE : Updating snakecdysis package (ref) using by frangiPANe if necessary

        python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main



1.2 Install frangiPANe tool
=================

Choose only one mode
-----------------

* in a cluster mode

::

    frangiPANe install_cluster -s slurm -e singularity

* or in local mode

::

    frangiPANe install_local

Add the prompt complementation
-----------------

::

    sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh


Download or build the singularity container in the container directory
-----------------

::

    # Download the container
    wget https://itrop.ird.fr/frangiPANe/frangiPANe.sif
    # OR build the container
    singularity build frangiPANe.sif frangiPANe.def

Checking if frangiPANe has been correctly installed
-----------------

::

    frangiPANe

**FrangiPANe structure**

::

    frangipane
    ├── docs
    │   ├── build
    │   ├── requirements.txt
    │   └── source
    ├── frangiPANe
    │   ├── containers
    │   │   ├── frangiPANe.def
    │   │   └── frangiPANe.sif
    │   ├── default_profile
    │   │   ├── cluster_config.yaml
    │   │   ├── config.yaml
    │   │   └── ...
    │   ├── frangiPANe-complete.sh
    │   ├── install_files
    │   │   ├── cluster_config_SLURM.yaml
    │   │   ├── config.yaml
    │   │   └── tools_path.yaml
    │   ├── main.py
    │   ├── module.py
    │   ├── report
    │   ├── schemas
    │   ├── snakefiles
    │   ├── snakemake_scripts
    │   │   ├── frangiPANe.py
    │   │   ├── generate_jb_frangiPANe.py
    │   │   ├── generate_jb.py
    │   │   └── __init__.py
    │   └── VERSION
    ├── LICENSE
    ├── pyproject.toml
    └── README.rst


II - Downloading a dataset to test frangiPANe
#################


::

   frangiPANe test_install -d path_to_directory_that_contains_data


III - Run FrangiPANe
#################


**local mode**

::

    frangiPANe -e
    frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2

**cluster mode**

::
    module load python/3.8.12

    frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml --cluster-config /scratch/tranchant/frangipane/frangiPANe/install_files/cluster_config_ITROP.yaml

::

    #!/bin/bash

    #SBATCH -J frangiPANe
    #SBATCH -o frangiPANe."%j".out
    #SBATCH -e frangiPANe."%j".err

    #SBATCH --mail-user christine.tranchant@ird.fr
    #SBATCH --mail-type=ALL

    #SBATCH -p normal
    #SBATCH -w node1
    #SBATCH -c 1 # number of nodes

    module load python/3.8.12
    module load singularity/4.0.1
    frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml

** example input**


IV - Outputs
#################

::

    tranchant@node1 tranchant]$ tree rice-output/
    rice-output/
    ├── 01-fastq
    │   ├── 01_mapped
    │   │   ├── panref
    │   │   └── ref
    │   └── 02-filtered
    │       └── ref
    ├── 02-assembly
    │   ├── 01-abyss
    │   ├── 02-filtered
    │   ├── 03-vecscreen
    │   └── 04-samples-merged
    ├── 03-clustering
    │   ├── 01-cd-hit
    │   └── 02-panreference
    ├── 04-stats
    │   ├── 01-fastq
    │   ├── 04-plots
    │   └── 04-summary
    ├── LOGS
    └── report


Authors
#################

* For version 2.0: *Sebastien Ravel and Christine Tranchant-Dubreuil (2024).*

* For version 0.1: *Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013.*

Licence
#################

-  Licencied under CeCill-C
   (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and
   GPLv3

-  Intellectual property belongs to IRD/UMR DIADE.

-  Copyright 2024

Reference
#################

.. [1] Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013..