diff --git a/Makefile b/Makefile index 981e34c..deab512 100644 --- a/Makefile +++ b/Makefile @@ -21,6 +21,8 @@ else SMK_PARAMS=--cores all --rerun-incomplete --printshellcmds --keep-going --use-conda --resources max_download_threads=10000000 max_io_heavy_threads=10000000 max_ram_mb=1000000000 $(SMK_CLUSTER_ARGS) endif +DOWNLOAD_PARAMS=--cores $(MAX_DOWNLOAD_THREADS) -j $(MAX_DOWNLOAD_THREADS) --restart-times $(DOWNLOAD_RETRIES) + ###################### ## General commands ## @@ -33,7 +35,7 @@ all: ## Run everything (the default rule) DIFF_CMD=diff -q <(gunzip --stdout output/reads_1___reads_2___reads_3___reads_4.sam_summary.gz | cut -f -3) <(xzcat data/reads_1___reads_2___reads_3___reads_4.sam_summary.xz | cut -f -3) test: ## Quick test using 3 batches - snakemake download $(SMK_PARAMS) -j 99999 --config batches=data/batches_small.txt # download is not benchmarked + snakemake download $(SMK_PARAMS) $(DOWNLOAD_PARAMS) --config batches=data/batches_small.txt # download is not benchmarked scripts/benchmark.py --log logs/benchmarks/test_match_$(DATETIME).txt "snakemake match $(SMK_PARAMS) --config batches=data/batches_small.txt nb_best_hits=1" scripts/benchmark.py --log logs/benchmarks/test_map_$(DATETIME).txt "snakemake map $(SMK_PARAMS) --config batches=data/batches_small.txt nb_best_hits=1" @if $(DIFF_CMD); then \ @@ -75,13 +77,13 @@ conda: ## Create the conda environments snakemake $(SMK_PARAMS) --conda-create-envs-only download: ## Download the assemblies and COBS indexes - snakemake download $(SMK_PARAMS) -j 99999 --restart-times $(DOWNLOAD_RETRIES) + snakemake download $(SMK_PARAMS) $(DOWNLOAD_PARAMS) download_asms: ## Download only the assemblies - snakemake download_asms_batches $(SMK_PARAMS) -j 99999 + snakemake download_asms_batches $(SMK_PARAMS) $(DOWNLOAD_PARAMS) download_cobs: ## Download only the COBS indexes - snakemake download_cobs_batches $(SMK_PARAMS) -j 99999 + snakemake download_cobs_batches $(SMK_PARAMS) $(DOWNLOAD_PARAMS) match: ## Match queries using COBS (queries -> candidates) scripts/benchmark.py --log logs/benchmarks/match_$(DATETIME).txt "snakemake match $(SMK_PARAMS)" @@ -110,7 +112,6 @@ report: ## Generate Snakemake report cluster_slurm: ## Submit to a SLURM cluster sbatch \ -c 10 \ - -p priority \ --mem=80GB \ -t 0-08:00:00 \ --wrap="make"