From e55b6d4f3e771982188b2fb51270ee8f036717fb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Nov 2019 17:51:07 +0100
Subject: [PATCH] training_dataset.config: fix psmn path
---
src/conda_psmn.sh | 6 +----
src/training_dataset.config | 44 ++++++++++++++++++-------------------
2 files changed, 23 insertions(+), 27 deletions(-)
mode change 100644 => 120000 src/conda_psmn.sh
diff --git a/src/conda_psmn.sh b/src/conda_psmn.sh
deleted file mode 100644
index 3a91a796..00000000
--- a/src/conda_psmn.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-CONDA_PATH=/Xnfs/lbmcdb/common/conda/
-source ${CONDA_PATH}init.sh
-CONDA_ENVS=${CONDA_PATH}/envs/
-
diff --git a/src/conda_psmn.sh b/src/conda_psmn.sh
new file mode 120000
index 00000000..cbb3d9b5
--- /dev/null
+++ b/src/conda_psmn.sh
@@ -0,0 +1 @@
+/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 43e8588a..deb62fec 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -118,8 +118,8 @@ profiles {
psmn {
process{
withName: build_synthetic_bed {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/bedtools_2.25.0"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
@@ -128,8 +128,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: fasta_from_bed {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/bedtools_2.25.0"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
@@ -138,8 +138,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: index_fasta {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/bowtie2_2.3.4.1"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -149,8 +149,8 @@ profiles {
penv = 'openmp16'
}
withName: mapping_fastq_paired {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/bowtie2_2.3.4.1"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -160,8 +160,8 @@ profiles {
penv = 'openmp16'
}
withName: bam_2_fastq_paired {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/samtools_1.7"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -171,8 +171,8 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam_paired {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/samtools_1.7"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -182,8 +182,8 @@ profiles {
penv = 'openmp16'
}
withName: index_bam_paired {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/samtools_1.7"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -193,8 +193,8 @@ profiles {
penv = 'openmp16'
}
withName: mapping_fastq_single {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/bowtie2_2.3.4.1"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -204,8 +204,8 @@ profiles {
penv = 'openmp16'
}
withName: bam_2_fastq_single {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/samtools_1.7"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -215,8 +215,8 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam_single {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/samtools_1.7"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
@@ -226,8 +226,8 @@ profiles {
penv = 'openmp16'
}
withName: index_bam_single {
- beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
- conda = "src/.conda_envs/samtools_1.7"
+ beforeScript = "source $baseDir/conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
--
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