Updated requirements, Snakefile

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}
@@ -60,17 +62,18 @@ 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}
  """
 
 #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)
 

additional_benchmarks/requirements.txt

@@ -2,4 +2,5 @@ snakemake
 numpy
 scipy
 matplotlib
+bedtools
 R