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cschin / Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index
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Submit a job with peregrine #39

Open RenzoTale88 opened 3 years ago

RenzoTale88 commented 3 years ago

Good day, I would like to test peregrine on some data I got in hand. I need to run it on our cluster environment, which support singularity. Now, to run it manually I can simply proceed with 

singularity run --bind $PWD:/mnt docker://cschin/peregrine:1.6.3 asm -h

Then, I can simply type yes and that would do the trick. However, when I submit it, I struggle to run it passing the stdin:

echo 'yes' | singularity run --bind $PWD:/mnt docker://cschin/peregrine:1.6.3 asm -h

This won't work because it won't recognise the input yes. Do you know of a way to overcome this?

Thanks Andrea

ASLeonard commented 3 years ago

I've found it to work by putting <<< "yes" at the end of the command, as in

singularity run --bind $PWD:/mnt docker://cschin/peregrine:1.6.3 asm -h <<< "yes"

This allowed me to submit it to a cluster without any interactive input.