location of scripts in singularity container

[JudithR]

Hi,

Thx for creating this tool and I'm curious to see how it performs on my dataset.

I'm using the prebuild singularity container, however I cannot find the location of the scripts required for preprocessing in the container. The required binaries for seqkit and porechops are also not available. Is this intentional?

Regards
Judith

[colindaven]

You should be able to find the location of any script within the PATH with the command which

singularity exec /path/containers/herro.sif herro inference

error: the following required arguments were not provided:
  -m <MODEL>
  -b <BATCH_SIZE>
  <READS>
  <OUTPUT>

Usage: herro inference -m <MODEL> -b <BATCH_SIZE> <READS> <OUTPUT>

For more information, try '--help'.

singularity exec /mnt/beegfs/scratch/bioinformatics/colin/containers/herro.sif which herro

/usr/bin/herro