init devcontainer file #128
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| ############################################################################### | |
| # | |
| # AUTHOR: Maciej_Bak | |
| # CONTACT: wsciekly.maciek@gmail.com | |
| # CREATED: 15-02-2022 | |
| # LICENSE: Apache_2.0 | |
| # | |
| ############################################################################### | |
| --- | |
| name: ci-pipeline | |
| on: push | |
| jobs: | |
| pipeline-testruns: | |
| runs-on: ubuntu-22.04 | |
| name: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: "true" | |
| - name: Setup miniconda & conda env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| auto-update-conda: true | |
| environment-file: environment.yml | |
| activate-environment: warlock | |
| auto-activate-base: false | |
| - name: Display all miniconda & env info | |
| shell: bash -l {0} | |
| run: | | |
| conda info -a | |
| conda list | |
| conda clean --all --yes | |
| - name: Print compiler path (Ubuntu) | |
| shell: bash -l {0} | |
| run: which g++ | |
| - name: Compile demon (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| g++ resources/demon_model/src/demon.cpp | |
| -o resources/demon_model/bin/demon | |
| -I/usr/share/miniconda3/envs/warlock/include | |
| -lm | |
| - name: Prepare internal conda envs (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| snakemake | |
| --snakefile="workflow/Snakefile" | |
| --configfile="tests/test1/config-Ubuntu.yml" | |
| --use-conda | |
| --conda-create-envs-only | |
| --cores 1 | |
| all | |
| - name: Install demonanalysis into the env (Ubuntu) | |
| shell: bash -l {0} | |
| run: | | |
| for file in .snakemake/conda/*.yaml; do | |
| if [ -f "$file" ]; then | |
| if grep -q "name: warlock-r" "$file"; then | |
| ENVPATH="${file%.yaml}" | |
| break | |
| fi | |
| fi | |
| done | |
| conda deactivate | |
| conda activate $ENVPATH | |
| Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)" || true | |
| Rscript -e "devtools::install('resources/demonanalysis', upgrade=TRUE)" || true | |
| # Run the tests sequentially; | |
| # This could be parallelized in the CI but setting up conda | |
| # is expensive; its faster to run the tests one-by-one. | |
| - name: Run the pipeline (test1) (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| bash warlock.sh | |
| --configfile tests/test1/config-Ubuntu.yml | |
| --environment local | |
| - name: Check outfiles (test1) (Ubuntu) | |
| shell: bash -l {0} | |
| working-directory: ./tests/test1 | |
| run: > | |
| md5sum -c output-Ubuntu.md5; | |
| [ -e output/analyses/00000000/muller.txt ] | |
| - name: Cleanup (test1) | |
| shell: bash -l {0} | |
| run: rm -rf tests/test1/output | |
| - name: Run the pipeline (test2) (Ubuntu) | |
| shell: bash -l {0} | |
| run: > | |
| bash warlock.sh | |
| --configfile tests/test2/config-Ubuntu.yml | |
| --environment local | |
| --cores 4 | |
| - name: Check outfiles (test2) (Ubuntu) | |
| shell: bash -l {0} | |
| working-directory: ./tests/test2 | |
| run: | | |
| md5sum -c output-Ubuntu.md5; | |
| for dir in $(find output/analyses -mindepth 1 -type d); do | |
| [ -e "$dir/muller.txt" ] | |
| done | |
| - name: Cleanup (test2) | |
| shell: bash -l {0} | |
| run: rm -rf tests/test2/output | |
| ... |