container for micro-sam

[CaroAMN]

Submitting a Container

Hi we would like to submit a container for the tool micro-sam which we would like to use in several nf-core pipelines.
Micro-sam is already in conda-forge but we cannot use this version of micro-sam because it cannot be run in a container. It contains some dependencies like napari that broke the container. Therefore we provide a conda.yml file with the adjusted dependencies.

We cannot change the conda package because our use case is more specific ( nf-core pipelines) and the tool would lose many functionalities for which it was designed but our pipelines don't need.

I opened the PR to ask if adding the container would be possible given this situation.

Check BioContainers' Dockerfile specifications

Checklist

1. Misc

• My tool doesn't exist in BioConda
• The image can be built

2. Metadata

• LABEL base_image
• LABEL version
• LABEL software.version
• LABEL about.summary
• LABEL about.home
• LABEL about.license
• MAINTAINER

3. Extra (optionals)

• I have written tests in test-cmds.txt
• LABEL extra.identifier
• LABEL about.documentation
• LABEL about.license_file
• LABEL about.tags

Check BioContainers' Dockerfile metadata

[mboudet]

Hi,

But we cannot use this version of micro-sam because it cannot be run in a container. It contains some dependencies like napari that broke the container.

Do you have more information on what doesn't work in the container, to make sure it will not occur here?

You should probably fix the version of the tool when pulling from github. Not really fond of the conda install, since deps will not be fixed, meaning rebuilding the container will not be really reproductible.
Any reason not to use the conda.yml provided in the git directly?

[biocontainers-bot]

about.license field is not in spdx list: https://spdx.org/licenses/, if it is a typo error, please fix it. If this is not a standard license, please specify Custom License and use about.license_file label to specify license location (in container or url).

[biocontainers-bot]

No biotools label defined, please check if tool is not already defined in biotools (https://bio.tools) and add extra.identifiers.biotools label if it exists. If it is not defined, you can ignore this comment.

[biocontainers-bot]

No test-cmds.txt (test file) present, skipping tests

[CaroAMN]

Hi,

But we cannot use this version of micro-sam because it cannot be run in a container. It contains some dependencies like napari that broke the container.

Do you have more information on what doesn't work in the container, to make sure it will not occur here?

We could not build the container when some packages like napari were installed. They were removed from the conda.yml that we provided here. With this conda env i could build and run the container. We think it's because those packages open a GUI. But for the purpose of automatic segmentation we don't need the GUI anyway.

You should probably fix the version of the tool when pulling from github. Not really fond of the conda install, since deps will not be fixed, meaning rebuilding the container will not be really reproducible. Any reason not to use the conda.yml provided in the git directly?

I fix this regarding the version. The conda.yml provided by the repo has the dependencies that cause the container to break while installing. The conda.yml that i included in the PR is the adjusted conda env and only excludes the dependencies that cause a problem while building the container.

But yes i see the problem with rebuilding the container. Right now i don't have a better idea how to approach the problem.
But open for any suggestions :)

[mboudet]

Ok. It's not that big of a deal to be honest.

Maybe storing something like the result of 'conda env export' after a successful install, and using it in the Dockerfile?