SOFT : DefenseFinder
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Site du soft: https://github.com/mdmparis/defense-finder
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LICENSE:
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GPL-v3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/DefenseFinder
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Load binaries and environment:
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-> Version v3.0.0

#Need Miniforge
module load devel/Miniforge/Miniforge3
module load bioinfo/DefenseFinder/3.0.0

To unload module, unload  in order:

module unload bioinfo/DefenseFinder/3.0.0
module unload devel/Miniforge/Miniforge3

Warning! By default all  cpus are used on the node. Don't forget to adjust --workers option of defense-finder command and --cpus-per-task option for Slurm.

Models path: /usr/local/bioinfo/src/DefenseFinder/DefenseFinder-v3.0.0/models

To run on GPU (prediction with ESM_DF and geneCLR_DF models):
#Need GPU. To submit on gpuq, see FAQ: https://bioinfo.genotoul.fr/index.php/faq/job_submission_faq/ -> How to use GPU node

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

To submit: sbatch test_DefenseFinder-v3.0.0.sh

See software documentation and our FAQ (https://vm-genoword.toulouse.inrae.fr/FAQ) for more informations.