search

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
481 stars 106 forks source link

Running the docker image in Singularity #1391

Open desmodus1984 opened 1 month ago

desmodus1984 commented 1 month ago

Hi,

I am using an HPC that has miniconda installed and singularity. I have downloaded the docker image but I am new with singularity and I don't know how to convert the docker parameters into singularity ones.

singularity exec -v $(pwd):/othersps --rm -it /home/juaguila/appz/cactus/cactus_v2.8.2.sif cactus /scratch/jfierst/jpac/ /othersps/seqfile /othersps/batref.hal

Since it seems to need the folder parameters, I start the job in the parent folder of othersps, where I run the command. I am running it in a conda environment with all the requirements of toil installed, and it has setuptools pip wheel.

Thanks;

Juan

glennhickey commented 1 month ago

I don't think singularity has --rm -it so you probably want to leave those out. Looks okay otherwise.