From dceeee6be02347c887a2e9da7a113b0c21551e60 Mon Sep 17 00:00:00 2001
From: Vince Buffalo <vsbuffalo@gmail.com>
Date: Sat, 18 May 2024 14:41:49 -0700
Subject: [PATCH] Updated requirements, Snakefile

---
 additional_benchmarks/Snakefile        | 21 ++++++++++++---------
 additional_benchmarks/requirements.txt |  1 +
 2 files changed, 13 insertions(+), 9 deletions(-)

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