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christine.tranchant_ird.fr authoredchristine.tranchant_ird.fr authored
.. 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
#####################
Install the frangiPANe python package
********************
Requirement
"""""""""""""""""
- `Git `_
- `Singularity `_
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
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..