SOFT : CulebrONT
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Site du soft: https://culebront-pipeline.readthedocs.io/en/latest/
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LICENSE:
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GPL-v3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/CulebrONT
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Load binaries and environment:
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-> Version v1.3.0

#Need Conda,snakemake  and Singularity 3.10.0+
unset PERL5LIB
module load system/Miniconda3-4.7.10 system/singularity-3.6.4

#Load snakemake in python-3.7
module load system/Python-3.7.4

Copy config files and adjust them :
/usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/config.yaml
/usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/cluster_config.yaml

Path to Snakefile: /usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/Snakefile
Path to slurm_wrapper.py and slurm_status.py:/usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/

#Example command for SLURM JOBS WITH USING WRAPPER in example directory /usr/local/bioinfo/src/CulebrONT/example_on_cluster/
snakemake --nolock --use-conda --use-singularity --singularity-args '--bind  /usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/' --cores -p -s /usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/Snakefile --latency-wait 60000000 --keep-going --restart-times 0 --rerun-incomplete --configfile /usr/local/bioinfo/src/CulebrONT/example_on_cluster/config.yaml --cluster "/usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/slurm_wrapper.py /usr/local/bioinfo/src/CulebrONT/example_on_cluster/config.yaml /usr/local/bioinfo/src/CulebrONT/example_on_cluster/cluster_config.yaml" --cluster-config /usr/local/bioinfo/src/CulebrONT/example_on_cluster/cluster_config.yaml --cluster-status "/usr/local/bioinfo/src/CulebrONT/CulebrONT_pipeline-v1.3.0/slurm_status.py"


Example directory for use on cluster:
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/usr/local/bioinfo/src/CulebrONT/example_on_cluster

To submit: sbatch test_CulebrONT_pipeline-v1.3.0.sh (TEST EN COURS, NON VALIDE)

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.