From 9a24a86d45d074d56df4c5da92a944388a706317 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 24 Oct 2018 15:10:35 +0200
Subject: [PATCH] training_dataset.config: update psmn config
---
src/training_dataset.config | 101 ++++++++++++++++++++++++++++--------
1 file changed, 78 insertions(+), 23 deletions(-)
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 20f3db36..3d804cca 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -41,53 +41,108 @@ profiles {
psmn {
process{
withname: build_synthetic_bed {
- beforeScript = "module purge; module load BEDtools/2.25.0"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BEDtools/2.25.0"
executor = "sge"
+ clusterOptions = "-m be -cwd -V"
cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: fasta_from_bed {
- beforeScript = "module purge; module load BEDtools/2.25.0"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BEDtools/2.25.0"
executor = "sge"
+ clusterOptions = "-m be -cwd -V"
cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: index_fasta {
- beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
withname: mapping_fastq_paired {
- beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
withname: bam_2_fastq_paired {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: sort_bam_paired {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: index_bam_paired {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: mapping_fastq_single {
- beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+ executor = "sge"
+ cpus = 16
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
}
withname: bam_2_fastq_single {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: sort_bam_single {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
withname: index_bam_single {
- beforeScript = "module purge; module load SAMtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "SAMtools/1.7"
+ executor = "sge"
+ cpus = 1
+ memory = "20GB"
+ time = "12h"
+ queue = 'monointeldeb128'
}
}
}
--
GitLab