In the following example the execution of a singularity container is demonstrated. The image (radinitio.sif) is located at the folder /mnt/big/containers/singularity/ and concerns a pipeline for the assessment of RADseq experiments. The executable is the radinitio command and the following example comes from the radinitio official tutorial (http://catchenlab.life.illinois.edu/radinitio/manual/#tutorial)
Please, take care that before the main command (“radinitio –simulate-all — …”), the container must be called:
“singularity exec /mnt/big/containers/singularity/radinitio.sif”
#!/bin/bash -l
#SBATCH --job-name=radinitio
#SBATCH --output=res.txt
#SBATCH --partition=batch
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mail-type=ALL
#SBATCH --mail-user=potant@hcmr.gr
module purge
module load singularity/3.7.1
singularity exec /mnt/big/containers/singularity/radinitio.sif radinitio --simulate-all --genome Gasterosteus_aculeatus.BROADS1.dna.toplevel.fa.gz \
--chromosomes chrom.list --out-dir ri_tutorial/ --library-type sdRAD --enz SbfI --n-pops 2 --n-seq-indv 10 --coverage 10
module unload singularity/3.7.1
