DIADE
frangiPANe_snake

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 snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
python3 -m pip install .
frangiPANe install_local
sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh
cd path2frangipane_directory/frangiPANe/frangiPANe/containers/

# Download the container
wget https://itrop.ird.fr/frangiPANe/frangiPANe.sif
frangiPANe  command
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A modular and interactive application to simplify  the construction of a panreference  using the map-then-assembly approach."

    Version Version 1.0

    @author: Sebastien Ravel and Christine Tranchant
    @email: christine.tranchant@ird.fr

    Please cite our github: https://forge.ird.fr/diade/frangipane

    Licencied under CeCill-C (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html)
    and GPLv3 Intellectual property belongs to IRD, CIRAD and authors.

    Documentation avail at: https://frangiPANe.readthedocs.io/en/latest/


    ** NOTE: This frangiPANe version (Version 1.0) is higher than the production version (There aren’t any releases), you are using a dev version


Usage: frangiPANe [OPTIONS] COMMAND [ARGS]...

Options:
  -r, --restore      Restore previous installation to use again "install_local" or "install_cluster"  [default: False]
  -e, --install_env  print Install path, Tools config, Install mode, Tools install mode, Current version, Latest version avail, Snakecdysis version
                     [default: False]
  -v, --version      Show the version and exit.
  -h, --help         Show this message and exit.

Commands:
  create_config        Create config.yaml for run
  edit_cluster_config  Edit cluster_config.yaml use by profile
  edit_tools           Edit own tools version
  run_cluster          Run workflow on HPC
  show_tools           show tools version
  test_install         Test frangiPANe cluster mode with "data_test"
frangiPANe edit_tools
 1 ## BUILD SINGULARITY IMAGES PATH
 2 ## PLEASE FILL IN SINGULARITY IMAGES PATH IF YOU HAVE CHOSEN INSTALL WITH ENV MODE SINGULARITY (option --env singularity)
 3 ## PLEASE FILL IN "ENVMODULES" SECTION IF YOU HAVE CHOSEN INSTALL WITH ENV MODE MODULES (option --env modules)
 4 ## WARNING!!! DO NOT ERASE LINES OR COMMENT THEM !  è_é
 5
 6 SINGULARITY:
 7
 8     TOOLS : '/scratch/tranchant/frangipane/frangiPANe/containers/frangiPANe.sif'
 9
10 # Is and exemple of tools path
11 ENVMODULE:
12     ABYSS : "abyss"
13     BWA : "bwa"
14     EA-UTILS : "ea-utils"
15     SAMTOOLS : "samtools"
16     ASSEMBLY-STATS : "assembly-stats"
17     CD-HIT : "cdhit"
18     FASTQ_STATS: "fastq_stats"
19     FASTQ_STATS: "fastq_stats"
20     NCBI-TOOLS: "ncbi-tools++"
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
frangiPANe test_install -d path_to_directory_that_contains_data
frangiPANe -e
frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2
frangiPANe edit_cluster_config
 1 __default__:
 2     cpus-per-task: 1
 3     mem-per-cpu: 6G
 4     partition: normal
 5     nodelist: node1
 6     output: '{log.output}_cluster'
 7     error: '{log.error}_cluster'
 8     job-name: '{rule}.{wildcards}'
 9
10 abyss:
11     cpus-per-task: 3
12
13 bwa_mem:
14     cpus-per-task: 4
15
16 samtools_view:
17     cpus-per-task: 3
18
19 samtools_flagstat:
20     cpus-per-task: 3
21
22 #vecscreen
23
24 #create_panref
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
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