scverse / scverse/scanpy

Generate BioContainer images

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Area – External Installation
Dominant language
Python
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Description

Hey,

we moved from conda-forge to Bioconda -> https://github.com/scverse/scanpy/issues/1169

Unfortunately, this comes at a cost which is highly relevant for pipeline building. nf-core wants to add support for scverse data structures: https://github.com/nf-core/scrnaseq/issues/68 The issue is that Bioconda autogenerates Docker & Singularity containers which Nextflow pipelines always use to provide support for all execution environments. conda-forge does not. The official Dockerhub is firstly stuck in an old version and, when used, it lacks the package procps that is used by nextflow to track execution.

How serious are the Bioconda issues? Can we resolve them and move back? I'd avoid always having to manage also our own container releases and love the automated container building by Bioconda.
I was also made aware by @apeltzer that bio specific tools should live in bioconda. Choosing to put them in conda-forge is not really desired.

@ivirshup @flying-sheep

CC @drpatelh @fmalmeida @apeltzer @grst

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 by reading the linked scanpy issue #1169 and nf-core/scrnaseq issue #68, then review the Bioconda-generated Docker and Singularity container behavior against the official Docker Hub image. Done means resolving the relevant Bioconda limitations or establishing a reliable image-generation path that supports Nextflow execution, including the procps package.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
bioinformatics, devops, infrastructure
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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