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Commit e04d4d3e authored by christine.tranchant_ird.fr's avatar christine.tranchant_ird.fr
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Adding documentation to install or run frangiPANe version 1.0

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......@@ -3,33 +3,32 @@ README
.. image:: docs/source/_images/frangiPANe.png
FrangiPANe
=========
FrangiPANe is a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.
It was previously developed as a modular and interactive application based on Jupyter Book.
It has now been recoded and integrated into a Snakemake pipeline.
How to install FrangiPANe ?
I - Installing FrangiPANe
-------------
Requirement
~~~~~~~~~~~~
**Requirement**
You have to install :
- [Git](https://git-scm.com/)
- [Singularity](https://...)
* git (https://git-scm.com/)
* singularity (https://...)
**Clone the git repository**
Clone the git repository
~~~~~~~~~~~~
::
git clone https://forge.ird.fr/diade/frangipane.git
Install the frangiPANe python package
~~~~~~~~~~~~
**Install the frangiPANe python package**
::
......@@ -38,52 +37,241 @@ Install the frangiPANe python package
python3 -m pip install -e .
Updating snakecdysis package (ref) using by frangiPANe
**Updating snakecdysis package (ref) using by frangiPANe if necessary**
::
```bash
python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
**Install frangiPANe tool**
Install frangiPANe tool in a cluster mode
~~~~~~~~~~~~
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 singularity container
Download or build the singularity container in the container directory
~~~~~~~~~~~
::
wget ...
# 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
II - Downloading a dataset to test frangiPANe
-------------README
========
.. image:: docs/source/_images/frangiPANe.png
FrangiPANe
=========
FrangiPANe is a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.
It was previously developed as a modular and interactive application based on Jupyter Book.
It has now been recoded and integrated into a Snakemake pipeline.
I - How to install FrangiPANe ?
-------------
**Requirement**
- [Git](https://git-scm.com/)
- [Singularity](https://...)
**Clone the git repository**
::
git clone https://forge.ird.fr/diade/frangipane.git
**Install the frangiPANe python package**
::
cd PATH_2_FRANGIPANE_DIRECTORY
python3 -m pip install -U pip setuptools build
python3 -m pip install -e .
**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
Checking if frangiPANe has been correctly installed
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
II - Download a dataset to test frangiPANe
-------------
::
frangiPANe test_install -d path_to_directory_that_contains_data
Run FrangiPANe
III - Run FrangiPANe
--------------
Download a dataset to test frangiPANe
~~~~~~~~~~~
**local mode**
::
frangiPANe -e
frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2
**cluster mode**
::
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
Authors
--------------
For version 2.0:
Sebastien Ravel and Christine Tranchant-Dubreuil (2024).
Previous versions
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.
- Written by Sebastien Ravel and Christine Tranchant-Dubreuil
- Copyright 2024
::
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**
::
frangiPANe test_install -d ../../data/
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
Authors
=======================
--------------
For version 2.0:
Sebastien Ravel and Christine Tranchant-Dubreuil (2024).
......@@ -93,7 +281,7 @@ Previous versions
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
......
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