SOFT : read_VAE
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Site du soft: https://github.com/CobiontID/read_VAE
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LICENSE:
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MIT

See software documentation for more informations.

Location: /usr/local/bioinfo/src/read_VAE
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Load binaries and environment:
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-> Version c3d684e

#Need Miniconda
module load devel/Miniconda/Miniconda3
module load bioinfo/read_VAE/c3d684e

#Need  kmer-counter, unique-kmer-counter,fastk-medians, Hexamer
module load bioinfo/kmer-counter/0.1.2 bioinfo/unique-kmer-counts/0.1.1 bioinfo/fastk-medians/0.1 bioinfo/hexamer/6308b73

To unload module, unload  in order:

module load bioinfo/read_VAE/c3d684e
module unload devel/Miniconda/Miniconda3


To use contig_tools: copy to your working directoryconfig.yml et adapt it  with your data. And copy experimental Snakefile and adapt it with your config.yml path file ( cluster Snakefile not OK for Slurm, just LSF cluster)
cp /usr/local/bioinfo/src/read_VAE/read_VAE-c3d684e/contig_tools/config.yml .
cp /usr/local/bioinfo/src/read_VAE/read_VAE-c3d684e/contig_tools/experimental/Snakefile .

snakemake --snakefile path_to_your_Snakefile  

To use read_tools: run each step individually ( cluster Snakefile not OK for Slurm, just LSF cluster). Scripts are loaded in your path with the module load.

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

To submit: sbatch test_read_VAE-c3d684e.sh

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