nf-core / nf-core/modules

Create biscuit tabix bgzip image

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Description

Have you checked the docs?
Description of the bug

I want to add new tools to an existing image hosted on quay.io.

Specifically, I want to add tabix and bgzip packages into biscuit image.

I tried this with no luck:

FROM quay.io/biocontainers/biscuit:1.2.0.20230130--he272189_0

RUN apt update && \
    apt install -y --no-install-recommends tabix bgzip && \
    apt clean && \
    rm -rf /var/lib/apt/lists/*

I get the below error:

 => ERROR [2/2] RUN apt update &&     apt install -y --no-install-recommends tabix bgzip &&     apt clean &&     rm -rf /var/lib/apt/lists/*                                                   0.3s
------                                                                                                                                                                                              
 > [2/2] RUN apt update &&     apt install -y --no-install-recommends tabix bgzip &&     apt clean &&     rm -rf /var/lib/apt/lists/*:
#5 0.177 /bin/sh: apt: command not found
------
executor failed running [/bin/sh -c apt update &&     apt install -y --no-install-recommends tabix bgzip &&     apt clean &&     rm -rf /var/lib/apt/lists/*]: exit code: 127

What is the Linux distribution in the images and how can I install new tools?

Thanks.

Command used and terminal output

No response

Relevant files

No response

System information

No response

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Dockerfile example and the quay.io/biocontainers/biscuit:1.2.0.20230130--he272189_0 image referenced in the issue. Inspect the image metadata and package-management setup; done means documenting the image's Linux distribution and the supported way to add tabix and bgzip. No repository files or tests are named.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, dockerfile, linux
Domain
devops, infrastructure
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
28/100

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