Container installation issues[BUG]

[sarapita]

Describe the bug
I pulled the latest container of hybracter
singularity pull --name quay.io-gbouras13-hybracter-v0.13.0.img

and then inspected it:
apptainer inspect quay.io-gbouras13-hybracter-v0.13.0.img

base.image: ubuntu:jammy
description: Unicycler is an assembly pipeline for bacterial genomes.
dockerfile.version: 1
license: https://github.com/rrwick/Unicycler/blob/main/LICENSE
maintainer: Erin Young
maintainer.email: eriny@utah.gov
maintainer1: Kelsey Florek
maintainer1.email: kelsey.florek@slh.wisc.edu
maintainer2: Curtis Kapsak
maintainer2.email: kapsakcj@gmail.com
org.label-schema.build-arch: amd64
org.label-schema.build-date: Tuesday_9_June_2026_14:29:4_BST
org.label-schema.schema-version: 1.0
org.label-schema.usage.apptainer.version: 1.4.4-1.el8
org.label-schema.usage.singularity.deffile.bootstrap: docker
org.label-schema.usage.singularity.deffile.from: quay.io/gbouras13/hybracter:v0.13.0
org.opencontainers.image.created: 2025-02-27T00:03:09.434Z
org.opencontainers.image.description: 📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
org.opencontainers.image.licenses: GPL-3.0
org.opencontainers.image.ref.name: ubuntu
org.opencontainers.image.revision: 15e0d9e3e16c6b8e28d5a8d4db50feed13e962af
org.opencontainers.image.source: https://github.com/StaPH-B/docker-builds
org.opencontainers.image.title: docker-builds
org.opencontainers.image.url: https://github.com/StaPH-B/docker-builds
org.opencontainers.image.version: master
software: Unicycler
software.version: 0.5.1
website: https://github.com/rrwick/Unicycler

Unfortunately, I can't access hybracter in it. Only Unicycler

I'm a bit confused. Quite new to containers so would be helpful to know if I'm doing anything obviously wrong.

Thanks

Best,
Sara

[gbouras13]

Hi @sarapita

Hybracter's container is built on top of the base image of Unicycler v0.5.1 from staphb (as unicycler can be tricky to install in conda). I have checked the latest container today - it seems fine

Do you mind trying

IMAGE_DIR="<the directory you want the .sif file to be in>"

apptainer pull --dir "$IMAGE_DIR" docker://quay.io/gbouras13/hybracter:v0.13.0

containerImage="$IMAGE_DIR/hybracter_v0.13.0.sif"

apptainer exec "$containerImage" hybracter --help

You should get

hybracter version 0.13.0



 _           _                    _            
| |__  _   _| |__  _ __ __ _  ___| |_ ___ _ __ 
| '_ \| | | | '_ \| '__/ _` |/ __| __/ _ \ '__|
| | | | |_| | |_) | | | (_| | (__| ||  __/ |   
|_| |_|\__, |_.__/|_|  \__,_|\___|\__\___|_|   
       |___/


Usage: hybracter [OPTIONS] COMMAND [ARGS]...

  For more options, run: hybracter command --help

Options:
  -h, --help  Show this message and exit.

Commands:
  install        Downloads and installs the plassembler database
  hybrid         Run hybracter with hybrid long and paired end short reads
  hybrid-single  Run hybracter hybrid on 1 isolate
  long           Run hybracter with only long reads
  long-single    Run hybracter long on 1 isolate
  test-hybrid    Test hybracter hybrid
  test-long      Test hybracter long
  config         Copy the system default config file
  citation       Print the citation(s) for hybracter
  version        Print the version for hybracter

[sarapita]

Hey @gbouras13,

Thanks for the quick reply.
I did what you suggested, but keep getting the same error
After

apptainer exec "$containerImage" hybracter --help

I got the following:
INFO: gocryptfs not found, will not be able to use gocryptfs
FATAL: "hybracter": executable file not found in $PATH

I'm using apptainer 1.3.4

[sarapita]

Hey @gbouras13,

I found a way to call hybracter after looking in the container:

apptainer exec "$containerImage" /opt/miniforge3/bin/hybracter --help

So I can at least use it now :)

[gbouras13]

Awesome @sarapita - I will still try to find out why hybracter isn't in $PATH (Seems to be apptainer specific?), but good that it is in there at least

Will leave this open for anyone seeing this

George