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…nd mm39 for deepCSA-core
…and remove legacy python container
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Pull Request Overview
This PR update for deepcsa_core v0.0.1-alpha focuses on dependency management, particularly by adding the pysam dependency to the deepcsa.yml file, aligning with container configuration and testing requirements.
- Added pysam==0.23.0 dependency
- Updated metadata and environment configurations for container execution
Files not reviewed (3)
- deepcsa_core/Dockerfile: Language not supported
- python_container/Dockerfile: Language not supported
- python_container/conda.yml: Language not supported
FedericaBrando
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FerriolCalvet
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Mar 28, 2025
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FerriolCalvet
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FerriolCalvet
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all looks good!
if the test in seqera works fine I guess it will be the final check.
FerriolCalvet
approved these changes
Mar 28, 2025
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The most important changes include adding metadata and environment configurations to the
deepcsa_coreDockerfile, updating dependencies, and removing the outdatedpython_containerDockerfile and its associated conda environment file.I need to test the user when running bgreference.
Ideally a container should never have root priviledge and should be run via a user. in this specific case the user is
mambauser.I am testing the deepcsa pipeline to be sure that the container is correctly working.
related with