diff --git a/additional_benchmarks/Snakefile b/additional_benchmarks/Snakefile index b79ceae..e8d3c81 100644 --- a/additional_benchmarks/Snakefile +++ b/additional_benchmarks/Snakefile @@ -32,9 +32,10 @@ rule granges_filter: output: "results/granges_filter__size_{size}.bed" benchmark: repeat("benchmarks/granges_filter__size_{size}.tsv", NREPS) resources: - runtime=30, - mem_mb_per_cpu=1800, - cpus_per_task=28 + partition="savio3", + runtime=300, + mem_mb=96000, + cpus_per_task=40 shell: """ {input.granges} filter --left {input.a} --right {input.b} --genome {input.genome} > {output} @@ -46,9 +47,10 @@ rule bedtools_intersect: output: "results/bedtools_intersect__size_{size}.bed" benchmark: repeat("benchmarks/bedtools_intersect__size_{size}.tsv", NREPS) resources: - runtime=30, - mem_mb_per_cpu=1800, - cpus_per_task=28 + partition="savio3", + runtime=300, + mem_mb=96000, + cpus_per_task=40 shell: """ bedtools intersect -a {input.a} -b {input.b} > {output} @@ -60,9 +62,10 @@ rule plyranges_join_overlap_inner: params: rscript = RSCRIPT benchmark: repeat("benchmarks/plyranges_join_overlap_inner__size_{size}.tsv", NREPS) resources: + partition="savio3", runtime=300, - mem_mb_per_cpu=1800, - cpus_per_task=28 + mem_mb=96000, + cpus_per_task=40 shell: """ {params.rscript} Rscripts/plyranges_join_overlap_inner.r {input.a} {input.b} > {output} @@ -70,7 +73,7 @@ rule plyranges_join_overlap_inner: #tools = ["bedtools_intersect", "granges_filter", "plyranges_join_overlap_inner"] tools = ["bedtools_intersect", "granges_filter"] -sizes = np.logspace(3, 9, 10).astype('int') +sizes = np.logspace(3, 7, 10).astype('int') all_benches = expand("results/{tool}__size_{size}.bed", tool=tools, size=sizes) diff --git a/additional_benchmarks/requirements.txt b/additional_benchmarks/requirements.txt index 4478738..7b80722 100644 --- a/additional_benchmarks/requirements.txt +++ b/additional_benchmarks/requirements.txt @@ -2,4 +2,5 @@ snakemake numpy scipy matplotlib +bedtools R