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Makefile
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.PHONY: run_all, run_all_slurm, prepare_envs
ADD_SINGULARITY_ARGS = #--singularity-args '\-u'
N_JOBS = 500
N_CORES = --cores 16
SNAKEMAKE_OPTS_SLURM = --profile slurm --use-singularity --jobs $(N_JOBS) $(ADD_SINGULARITY_ARGS) \
--use-conda --conda-frontend mamba
SNAKEMAKE_OPTS = --use-conda --conda-frontend mamba --use-singularity $(ADD_SINGULARITY_ARGS)\
$(N_CORES)
SNAKEMAKE_PREPARE = --use-conda --use-singularity \
$(N_CORES) --conda-create-envs-only
SNAKEMAKE_BIN = snakemake
run_all:
cd subworkflows/bf_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS)
cd subworkflows/phys_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS)
cd subworkflows/oexp_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS)
cd subworkflows/phys_analysis && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS)
cd subworkflows/oexp_analysis && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS)
run_all_slurm:
cd subworkflows/bf_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS_SLURM)
cd subworkflows/phys_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS_SLURM)
cd subworkflows/oexp_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS_SLURM)
cd subworkflows/phys_analysis && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS_SLURM)
cd subworkflows/oexp_analysis && $(SNAKEMAKE_BIN) $(SNAKEMAKE_OPTS_SLURM)
prepare_envs:
cd subworkflows/bf_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_PREPARE)
cd subworkflows/phys_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_PREPARE)
cd subworkflows/oexp_preproc && $(SNAKEMAKE_BIN) $(SNAKEMAKE_PREPARE)
cd subworkflows/phys_analysis && $(SNAKEMAKE_BIN) $(SNAKEMAKE_PREPARE)
cd subworkflows/oexp_analysis && $(SNAKEMAKE_BIN) $(SNAKEMAKE_PREPARE)