4.5 Example execution:
Using the 2 fastqc available files, process them outside and inside the mounted directory.
Let’s use our
fastqc.sif image file and we place it in $HOME
# Let's create a dummy directory mkdir $HOME/scratch # Let's copy contents of testdata in scratch singularity exec fastqc.sif fastqc scratch/*fastq.gz # Check you have some HTMLs there. Remove them rm scratch/*html # Let's use shell singularity shell fastqc.sif > cd scratch > fastqc *fastq.gz > exit # Check you have some HTMLs there. Remove them singularity exec -B ./scratch:/fastqcdir fastqc.sif fastqc /fastqcdir/*fastq.gz # What happens here! singularity exec -B ./scratch:/fastqcdir fastqc.sif bash -c 'fastqc /fastqcdir/*fastq.gz'