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Alex Kanitz authored
- add 3 separate Conda environment files for installing - essential dependencies without Singularity (most users) - essential dependencies including Singularity (root users on Linux only) - non-essential dependencies (required for tests etc.) - install Python dependencies via `pip` _within_ Conda environment to avoid #56 - update Conda-based installation instructions - describe usage of different environment files - add supported OS versions (macOS not yet added, because only installation works) - update CI config to use same setup (based on Miniconda Docker image)
Alex Kanitz authored- add 3 separate Conda environment files for installing - essential dependencies without Singularity (most users) - essential dependencies including Singularity (root users on Linux only) - non-essential dependencies (required for tests etc.) - install Python dependencies via `pip` _within_ Conda environment to avoid #56 - update Conda-based installation instructions - describe usage of different environment files - add supported OS versions (macOS not yet added, because only installation works) - update CI config to use same setup (based on Miniconda Docker image)
.gitlab-ci.yml 741 B
image: continuumio/miniconda3:4.7.12
before_script:
- apt update && apt install -y gcc
- conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV
- conda env create -f install/environment.root.yml
- conda activate rnaseq_pipeline && echo $CONDA_DEFAULT_ENV
- conda env update -f install/environment.dev.yml
test:
script:
# add code quality tests here
# add unit tests here
# add script tests here
- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
- bash tests/test_create_rule_graph/test.sh
- bash tests/test_integration_workflow/test.local.sh