changing the $HOME folder in a singularity container

Question

please would you advise:

given a singularity container, how can I copy the files from the local drive to the singularity container?

I am using a singularity container that is described at:

 https://hub.docker.com/r/tobneu/slamdunk 

(and from the docker image i have made a singularity image for a SLURM cluster)

I have searched the stackoverflow for answers, however, i have found the answer only to the reverse question ie copying the files from the singularity container to the local drive.

https://stackoverflow.com/questions/59736299/transferring-files-from-the-singularity-container-into-the-local-directory

thanks a lot,

bogdan

Answer 1

As mentioned on your previous question , singularity has the -H / --home command line parameter.

singularity exec -H /labs/zzz/data my_image.sif bash -c 'echo "HOME=$HOME";echo "PWD=$PWD"'
# HOME=/labs/zzz/data
# PWD=...

Answer 2

I shall rephrase the question though, as i have noted that the singularity container sees the $HOME folder that i do have on a SLURM cluster (ie /home/btanasa ).

Please, if I may re-phrase the question: how shall i change the $HOME folder that the singularity container sees, for example /labs/zzz/data ? thanks a million !

Answer 3

Finally, i have got it to work. Shall anyone need to know the answer to the question in the title, it is outlined below by using --bind and --home:

singularity exec \
--bind /local/scratch/btanasa:/output8 \
--home /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021:/home \
/labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021/SLAMDUNK_SINGULARITY/slamdunk_latest.sif slamdunk all \
-r GRCm38.primary_assembly.genome.fa \
-b 3UTRs_vM14_github_repository.27aug2020.sortdesc.LONG.with.SYMBOLS.to.use.bed \ -o /output8 \
-t 4 \
./8_R1_001.fastq.gz