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Baysor module #7270

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Baysor module #7270

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sebgoti
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@sebgoti sebgoti commented Jan 7, 2025

Attempting to do my first module’s contribution, so some things might be improved. I also know that @khersameesh24 wanted to work on this module.

Quick note on tests:

  • Right now there is no main.nf.test.snap file since the module’s output is non-deterministic. I was not sure on what is the best way to tackle this, so any feedback is really appreciated.

process BAYSOR {
tag '$meta.id'
label 'process_high_memory'
container "docker.io/segonzal/baysor:0.7.1"
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@khersameesh24 khersameesh24 Jan 7, 2025

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@sebgoti, ask a core team member to get the baysor image into nf-core
You can also refer to Docker image if the image size is too large

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@khersameesh24, indeed my current image is very large (~15 GB). I could refer to yours but I wanted to use the latest version (0.7.1). Could you help me figuring out how to reduce the size? Here is how I build the image:
FROM quay.io/pypa/manylinux2014_x86_64

WORKDIR /app
RUN yum install -y unzip
RUN curl -O -L https://github.com/kharchenkolab/Baysor/releases/download/v0.7.1/baysor-x86_x64-linux-v0.7.1_build.zip
RUN unzip baysor-x86_x64-linux-v0.7.1_build.zip
RUN mv bin unzip
RUN mv unzip/baysor/* .
RUN rm -rf unzip
RUN rm baysor-x86_x64-linux-v0.7.1_build.zip
ENV PATH="/app/bin:$PATH"

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The docker image from [Baysor Dockerhub](docker pull vpetukhov/baysor:v0.7.0) can also be referred to in this case

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I just checked and my image with the latest version has a compressed size of 5.41 GB, this one (vpetukhov/baysor:v0.7.0) is 2.12 GB. If this difference is not significant I would rather keep the latest version since it fixes some issues from the tool.

def VERSION = "0.7.1"

"""
/app/bin/baysor run ${transcripts_csv} -c ${config_toml} $args
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In the docker image, add the baysor executable to PATH

when:
task.ext.when == null || task.ext.when

script:
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@khersameesh24 khersameesh24 Jan 7, 2025

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add the following code snippet to have a check for conda

if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
        error "Baysor module does not support Conda. Please use Docker / Singularity / Podman instead."
    }

@famosab
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famosab commented Feb 6, 2025

Is there anything that speaks against putting this tool on bioconda? :)

@khersameesh24
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khersameesh24 commented Feb 6, 2025

Hi @famosab , I tried to get baysor running within bioconda, but after multiple failed attempts decided to go just with a docker container. As per the license, I don't think its an issue.

@sebgoti sebgoti mentioned this pull request Feb 11, 2025
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@FloWuenne
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Hey @sebgoti ,
amazing to see your first contribution to nf-core/modules 🚀 !

  • Do you still need someone from the core team to upload the images to quay.io or you simply need to update the container reference in the module?
  • Will you be able to finalize this PR during the upcoming hackathon?

@sebgoti
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sebgoti commented Mar 11, 2025

Hi @FloWuenne, I think that @khersameesh24 already uploaded the image to quay.io :) And yes, the idea is to wrap this up at the hackathon. We are now only missing a couple of tests.

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4 participants