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Commit e55b6d4f authored by Laurent Modolo's avatar Laurent Modolo
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training_dataset.config: fix psmn path

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src/conda_psmn.sh deleted 100644 → 0
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#!/bin/sh
CONDA_PATH=/Xnfs/lbmcdb/common/conda/
source ${CONDA_PATH}init.sh
CONDA_ENVS=${CONDA_PATH}/envs/
src/conda_psmn.sh 0 → 120000
+ 1
− 5
View file @ e55b6d4f
/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file
src/training_dataset.config
+ 22
− 22
View file @ e55b6d4f
...@@ -118,8 +118,8 @@ profiles { ...@@ -118,8 +118,8 @@ profiles {
psmn { psmn {
process{ process{
withName: build_synthetic_bed { withName: build_synthetic_bed {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/bedtools_2.25.0" conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1 cpus = 1
...@@ -128,8 +128,8 @@ profiles { ...@@ -128,8 +128,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
} }
withName: fasta_from_bed { withName: fasta_from_bed {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/bedtools_2.25.0" conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1 cpus = 1
...@@ -138,8 +138,8 @@ profiles { ...@@ -138,8 +138,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
} }
withName: index_fasta { withName: index_fasta {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/bowtie2_2.3.4.1" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -149,8 +149,8 @@ profiles { ...@@ -149,8 +149,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: mapping_fastq_paired { withName: mapping_fastq_paired {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/bowtie2_2.3.4.1" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -160,8 +160,8 @@ profiles { ...@@ -160,8 +160,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: bam_2_fastq_paired { withName: bam_2_fastq_paired {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/samtools_1.7" conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -171,8 +171,8 @@ profiles { ...@@ -171,8 +171,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: sort_bam_paired { withName: sort_bam_paired {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/samtools_1.7" conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -182,8 +182,8 @@ profiles { ...@@ -182,8 +182,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: index_bam_paired { withName: index_bam_paired {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/samtools_1.7" conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -193,8 +193,8 @@ profiles { ...@@ -193,8 +193,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: mapping_fastq_single { withName: mapping_fastq_single {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/bowtie2_2.3.4.1" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -204,8 +204,8 @@ profiles { ...@@ -204,8 +204,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: bam_2_fastq_single { withName: bam_2_fastq_single {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/samtools_1.7" conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -215,8 +215,8 @@ profiles { ...@@ -215,8 +215,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: sort_bam_single { withName: sort_bam_single {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/samtools_1.7" conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -226,8 +226,8 @@ profiles { ...@@ -226,8 +226,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: index_bam_single { withName: index_bam_single {
beforeScript = "$workflow.projectDir/src/conda_psmn.sh" beforeScript = "source $baseDir/conda_psmn.sh"
conda = "src/.conda_envs/samtools_1.7" conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
......
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