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Container for scsplit #565

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IreneRobles opened this issue Mar 22, 2024 · 4 comments
Closed

Container for scsplit #565

IreneRobles opened this issue Mar 22, 2024 · 4 comments

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@IreneRobles
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I am building a nf-core module for scsplit
Trying to follow guidelines, I would like to add a scsplit docker to biocontainers, so it can be imported by my module

Software URL: https://github.com/jon-xu/scSplit

This docker image would work:

FROM python:3.9 as base

ARG SCSPLIT_VERSION="1.0.8"

RUN apt-get update && apt-get install -y python3-pip git

RUN pip install "setuptools==57.5.0" wheel numpy pandas pysam pyvcf3 scikit-learn scipy statistics 
RUN wget https://github.com/jon-xu/scSplit/archive/refs/tags/v${SCSPLIT_VERSION}.tar.gz -O /opt/scsplit.gz && \
    tar xvzf /opt/scsplit.gz -C /opt && \
    rm /opt/scsplit.gz

ENV PATH="${PATH}:/opt/scSplit-${SCSPLIT_VERSION}"

CMD [ "bash" ]
@IreneRobles IreneRobles mentioned this issue Mar 22, 2024
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@IreneRobles
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Attempting to suggest a docker image, I created this pull request: #564

@mboudet
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mboudet commented Mar 29, 2024

Ok, it seems this package already exists in bioconda (https://bioconda.github.io/recipes/scsplit/README.html)

As such, there is already a docker image available here: https://quay.io/repository/biocontainers/scsplit

@IreneRobles
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IreneRobles commented Apr 2, 2024 via email

@mboudet
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mboudet commented Apr 2, 2024

Hmm, seems like the conda install is missing some dependencies (like numpy) anyway.
Beyond that, the docker image is not broken, it's just how the tool works when you install it with pip (either you import it in python, or you manually call '/usr/local/lib/python3.12/site-packages/scSplit/scSplit'. I suppose the conda recipe could have added this file in the path.

In any case, to avoid confusion, we do not add tools already existing in bioconda in this repository, so you'll have to check on the bioconda side to fix the recipe (and get a working docker image)

@mboudet mboudet closed this as completed May 7, 2024
@mboudet mboudet closed this as not planned Won't fix, can't repro, duplicate, stale May 7, 2024
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feat: dockerfile for scsplit IreneRobles/containers
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@mboudet @IreneRobles