Commit a52ac9b0 authored by James Kolpack's avatar James Kolpack Committed by James G. Kolpack

Add switching between SLURM and TORQUE queuing systems.

Add config file for queuing parameters.
Removal of mail parameter - it can be configured via config file.
Removal of SLURM specific directives from pipeline modules.
parent cf77580f
#!/bin/bash -l
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 0:30:00
#SBATCH --mail-type=ALL
## stop on error but be verbose
set -e
......
#!/bin/bash -l
#SBATCH -p core -n 1
#SBATCH -t 0-01:00:00
#SBATCH --mail-type=ALL
usage() {
echo "usage: `basename $0` <fastq>
......
#!/bin/bash -l
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 8:00:00
#SBATCH --mail-type=ALL
## -A and --mail-user set in the submit job
## stop on error
set -ex
......
This diff is collapsed.
......@@ -4,11 +4,6 @@
## but consider if we want that when reporting the Chimeric SAM (i.e. for merging the files, we would not want the reads to be part of the SAM...
## the good thing with outputting to SAM is that it can be readily piped into samtools -bs - | samtools sort - filename
#SBATCH -p core
#SBATCH -n 8
#SBATCH -t 0-02:00:00
#SBATCH --mail-type=ALL
#################
## Build geneModel
#################
......
#!/bin/bash -l
#SBATCH -p node
## for large files
## we don't need the proc but the mem
## we could give that as param
#SBATCH -n 16
## time too for large files
#SBATCH -t 12:00:00
#SBATCH --mail-type=ALL
## mail-user and A have to be set in the submit script
## stop on error
set -e
......
#!/bin/bash -l
#SBATCH -p node
#SBATCH -n 16
#SBATCH -t 3-00:00:00
#SBATCH --mail-type=ALL
## abort on error
set -e
......
#Example SLURM configuration for RNA seq pipeline
global_batch_args='--mail-type ALL'
fastqc_batch_args='--partition core --ntasks 1 -t 0:30:00'
fastqvalidator_batch_args='--partition core --ntasks 1 -t 1:00:00'
sortmerna_batch_args='--partition node --ntasks 16 -t 12:00:00'
trimmomatic_batch_args='--partition node --ntasks 16 -t 3-00:00:00'
star_batch_args='--partition core --ntasks 8 -t 2:00:00'
htseq_batch_args='--partition core --ntasks 1 -t 8:00:00'
# Example SLURM configuration for RNA seq pipeline
global_batch_args=' '
fastqc_batch_args='-q core -l procs=1 -l walltime=0:30:00'
fastqvalidator_batch_args='-q core -l procs=1 -l walltime=1:00:00'
sortmerna_batch_args='-q node -l procs=16 -l walltime=12:00:00'
trimmomatic_batch_args='-q node -l procs=16 -l walltime=3:00:00:00'
star_batch_args='-q core -l procs=8 -l walltime=2:00:00'
htseq_batch_args='-q core -l procs=1 -l walltime=8:00:00'
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment