From ef2f3fe2aaea28bf5b531d925ea09781bd4cf138 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 11 Oct 2018 16:40:45 +0200
Subject: [PATCH] SNP_calling.config: fix module load for SGE
---
src/SNP_calling.config | 42 ++++++++++++++++++++++++++++--------------
1 file changed, 28 insertions(+), 14 deletions(-)
diff --git a/src/SNP_calling.config b/src/SNP_calling.config
index 39e0d7b..1ca9ac2 100644
--- a/src/SNP_calling.config
+++ b/src/SNP_calling.config
@@ -52,7 +52,8 @@ profiles {
queueSize = 1000
pollInterval = '60sec'
withName: adaptor_removal {
- beforeScript = "module purge; module load cutadapt/1.14"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "cutadapt/1.14"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -60,7 +61,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: trimming {
- beforeScript = "module purge; module load UrQt/d62c1f8"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "UrQt/d62c1f8"
executor = "sge"
cpus = 16
memory = "5GB"
@@ -69,7 +71,8 @@ profiles {
penv = 'openmp16'
}
withName: filter_fasta {
- beforeScript = "module purge; module load bioawk/1.0"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "bioawk/1.0"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -77,7 +80,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: index_fasta {
- beforeScript = "module purge; module load Bowtie2/2.3.4.1; module load sambamba/0.6.7; module load samblaster/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "Bowtie2/2.3.4.1:sambamba/0.6.7:samblaster/0.1.24"
executor = "sge"
cpus = 1
memory = "30GB"
@@ -85,7 +89,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: mapping_fastq {
- 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:sambamba/0.6.7:samblaster/0.1.24"
executor = "sge"
cpus = 16
memory = "30GB"
@@ -94,7 +99,8 @@ profiles {
penv = 'openmp16'
}
withName: merge_bam {
- beforeScript = "module purge; module load sambamba/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
executor = "sge"
cpus = 16
memory = "30GB"
@@ -103,7 +109,8 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam {
- beforeScript = "module purge; module load sambamba/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
executor = "sge"
cpus = 16
memory = "30GB"
@@ -112,7 +119,8 @@ profiles {
penv = 'openmp16'
}
withName: index_bam {
- beforeScript = "module purge; module load sambamba/0.6.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "sambamba/0.6.7"
executor = "sge"
cpus = 16
memory = "30GB"
@@ -121,7 +129,8 @@ profiles {
penv = 'openmp16'
}
withName: index2_fasta {
- beforeScript = "module purge; module load GATK/4.0.8.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "GATK/4.0.10.1"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -129,7 +138,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: index3_fasta {
- 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"
@@ -137,7 +147,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: samtools_SNP_tumor {
- beforeScript = "module purge; module load BCFtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BCFtools/1.7"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -145,7 +156,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: samtools_SNP_norm {
- beforeScript = "module purge; module load BCFtools/1.7"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "BCFtools/1.7"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -153,7 +165,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: vcf_to_csv_tumor {
- beforeScript = "module purge; module load GATK/4.0.8.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "GATK/4.0.10.1"
executor = "sge"
cpus = 1
memory = "20GB"
@@ -161,7 +174,8 @@ profiles {
queue = 'monointeldeb128'
}
withName: vcf_to_csv_norm {
- beforeScript = "module purge; module load GATK/4.0.8.1"
+ beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+ module = "GATK/4.0.10.1"
executor = "sge"
cpus = 1
memory = "20GB"
--
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