From 8b7e3616ff6a94f24a768deac5ed2aee73753b7d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 12 May 2022 16:31:20 +0200
Subject: [PATCH] working config and daemon job for in2p3
---
src/in2p3.pbs | 50 +++++++++++++++++++--------------------------
src/nextflow.config | 19 +++++++++--------
2 files changed, 31 insertions(+), 38 deletions(-)
diff --git a/src/in2p3.pbs b/src/in2p3.pbs
index 7f929a7e..9fd73c76 100644
--- a/src/in2p3.pbs
+++ b/src/in2p3.pbs
@@ -1,31 +1,23 @@
-#! /usr/local/bin/bash -l
-#####################################
-# job script example with GE options
-#####################################
-#$ -q demon
-#$ -l demon=1
-#$ -P P_lbmc
-#$ -N nf_pipe
-#$ -o /sps/lbmc/lmodolo/logs/ # change to your username !
-#$ -e /sps/lbmc/lmodolo/logs/ # change to your username !
-#$ -r n # relaunch y/n
-#$ -M laurent.modolo@ens-lyon.fr # change to your mail !
-#$ -m be ## send an email when the job starts and ends
-#$ -l os=cl7 ## choose OS
-#$ -l sps=1 ## acces /sps directory
-#####################################
+#!/bin/sh
-NF_VERSION=19.10
-NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
-# change to your username
-SCRATCH=/sps/lbmc/lmodolo/
-# change to your project / pipeline !
-PIPELINE=${SCRATCH}/nextflow/src/training_dataset.nf
-# change to your project / pipeline !
-CONFIG=${SCRATCH}/nextflow/src/training_dataset.config
+#SBATCH --job-name=nextflow
-${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
---fasta "${SCRATCH}/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
---fastq_single "${SCRATCH}/nextflow/data/tiny_dataset/fastq/tiny2_S.fastq.gz" \
---chromosome "X" --start 5305683 --stop 5333928 -resume \
--w "${SCRATCH}"
+#SBATCH --ntasks=1
+#SBATCH --output=results/nextflow_%j.log
+#SBATCH --licenses=sps
+
+####################################
+
+# change to your path
+SCRATCH=/sps/lbmc/lmodolo/nextflow
+NXF_TEMP=/sps/lbmc/lmodolo/nextflow/tmp/
+mkdir -p ${NXF_TEMP}
+
+${SCRATCH}/nextflow run ${SCRATCH}/src/solution_RNASeq.nf -profile ccin2p3 \
+--fastq "${SCRATCH}/data/tiny_dataset/fastq/*_R{1,2}.fastq" \
+--fasta "${SCRATCH}/data/tiny_dataset/fasta/tiny_v2.fasta" \
+--bed "${SCRATCH}/data/tiny_dataset/annot/tiny.bed" \
+-ansi-log \
+-w "${SCRATCH}/work/"
+
+wait
diff --git a/src/nextflow.config b/src/nextflow.config
index 23ef0d8e..f848cda0 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -125,8 +125,8 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
- singularity.cacheDir = "$baseDir/.singularity_in2p3/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ singularity.cacheDir = "$baseDir/../bin/"
+ singularity.runOptions = "--bind /pbs,/sps,/scratch,/tmp"
process{
maxRetries = 3
withLabel: big_mem_mono_cpus {
@@ -134,39 +134,40 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "slurm"
- clusterOptions = "--partition=htc --licenses=sps"
+ clusterOptions = "--licenses=sps"
cpus = 1
memory = "8GB"
+ queue = "htc"
}
withLabel: big_mem_multi_cpus {
- container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "slurm"
- clusterOptions = "--partition=htc --licenses=sps"
+ clusterOptions = "--licenses=sps"
cpus = 1
memory = "8GB"
- queue = "huge"
+ queue = "htc"
}
withLabel: small_mem_mono_cpus {
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "slurm"
- clusterOptions = "--partition=htc --licenses=sps"
+ clusterOptions = "--licenses=sps"
cpus = 1
memory = "8GB"
+ queue = "htc"
}
withLabel: small_mem_multi_cpus {
- container = "lbmc/urqt:d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "slurm"
- clusterOptions = "--partition=htc --licenses=sps"
+ clusterOptions = "--licenses=sps"
cpus = 1
memory = "8GB"
+ queue = "htc"
}
}
}
--
GitLab