From 7abb9126ace46fcfb7c8432853aeae6bfb9ef4f7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 25 Nov 2022 11:10:34 +0100
Subject: [PATCH] src/RibosomeProfiling.config: add slurm profile
---
src/RibosomeProfiling.config | 51 ++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
diff --git a/src/RibosomeProfiling.config b/src/RibosomeProfiling.config
index b4abd97e..bdb96932 100644
--- a/src/RibosomeProfiling.config
+++ b/src/RibosomeProfiling.config
@@ -1,4 +1,55 @@
profiles {
+ slurm {
+ process{
+ withName: trimming {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/cutadapt_2.4"
+ executor = "slurm"
+ cpus = 1
+ memory = "128GB"
+ time = "24h"
+ clusterOptions = "--partition=Lake"
+ }
+ withName: rRNA_removal {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
+ executor = "slurm"
+ cpus = 32
+ memory = "192GB"
+ time = "24h"
+ clusterOptions = "--partition=Lake"
+ }
+ withName: hisat2_human {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "hisat2/2.1.0:samtools/1.7"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ executor = "slurm"
+ cpus = 32
+ memory = "64GB"
+ time = "24h"
+ clusterOptions = "--partition=Lake"
+ }
+ withName: index_bam {
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
+ executor = "slurm"
+ cpus = 1
+ memory = "20GB"
+ time = "24h"
+ clusterOptions = "--partition=Lake"
+ }
+ withName: counting {
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "htseq/0.11.2"
+ executor = "slurm"
+ cpus = 1
+ memory = "20GB"
+ time = "24h"
+ clusterOptions = "--partition=Lake"
+ }
+ }
+ }
sge {
process{
withName: trimming {
--
GitLab