From ffb23d50b81505cb4022b6c6e4dbe6a2c73fdf1e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Nov 2019 17:12:30 +0100
Subject: [PATCH] training_dataset.config: update config to match latest
changes
---
src/training_dataset.config | 97 +++++++++++++++++++------------------
1 file changed, 49 insertions(+), 48 deletions(-)
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 96add9d1..9c831b34 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -4,112 +4,113 @@ profiles {
docker.enabled = true
process {
withName: build_synthetic_bed {
- container = "bedtools:2.25.0"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: fasta_from_bed {
- container = "bedtools:2.25.0"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: index_fasta {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_paired {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_paired {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_paired {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_paired {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_paired {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: mapping_fastq_single {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_single {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_single {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_single {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_single {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
}
singularity {
singularity.enabled = true
+ singularity.cacheDir = "./bin/"
process {
withName: build_synthetic_bed {
- container = "file://bin/bedtools:2.25.0.img"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: fasta_from_bed {
- container = "file://bin/bedtools:2.25.0.img"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: index_fasta {
- container = "file://bin/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_single {
- container = "file://bin/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_paired {
- container = "file://bin/bowtie2:2.3.4.1.img"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_paired {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_paired {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_paired {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_paired {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: bam_2_fastq_single {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_single {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_single {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_single {
- container = "file://bin/samtools:1.7.img"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
@@ -117,8 +118,8 @@ profiles {
psmn {
process{
withName: build_synthetic_bed {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "bedtools/2.25.0"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
@@ -127,8 +128,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: fasta_from_bed {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "bedtools/2.25.0"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
@@ -137,8 +138,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: index_fasta {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "bowtie2/2.3.4.1"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -148,8 +149,8 @@ profiles {
penv = 'openmp16'
}
withName: mapping_fastq_paired {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "bowtie2/2.3.4.1:samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -159,8 +160,8 @@ profiles {
penv = 'openmp16'
}
withName: bam_2_fastq_paired {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -170,8 +171,8 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam_paired {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -181,8 +182,8 @@ profiles {
penv = 'openmp16'
}
withName: index_bam_paired {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -192,8 +193,8 @@ profiles {
penv = 'openmp16'
}
withName: mapping_fastq_single {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "bowtie2/2.3.4.1:samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -203,8 +204,8 @@ profiles {
penv = 'openmp16'
}
withName: bam_2_fastq_single {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -214,8 +215,8 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam_single {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -225,8 +226,8 @@ profiles {
penv = 'openmp16'
}
withName: index_bam_single {
- beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "samtools/1.7"
+ beforeScript = "./src/conda_psmn.sh"
+ conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
--
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