SOFT : snakePipes
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Site du soft: https://github.com/maxplanck-ie/snakepipes
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LICENSE:
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MIT

See software documentation for more informations.

Location: /usr/local/bioinfo/src/snakePipes
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Load binaries and environment:
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-> Version v2.5.1

#Need Miniconda3-4.7.10
module load system/Miniconda3-4.7.10
module load bioinfo/snakePipes-2.5.1

Be careful, to unload, not use module purge but in order:

module unload bioinfo/snakePipes-2.5.1
module unload system/Miniconda3-4.7.10

organismsDir: /usr/local/bioinfo/src/snakePipes/snakePipes-2.5.1/organisms

!!! Be careful: organismsDir are writable for all (for yaml file and index files required by various tools within snakePipes. You can choose other directory with --userYAML and -o option of createIndices command)
The necessary CONDA environment are re-created each time a pipeline is launched. Don't forget to use --snakemakeOptions= --use-conda --conda-prefix <path_to_user_working_dir> to create it.

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

To submit: sbatch test_snakePipes-2.5.1.sh

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