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v0.10.0
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| name: Lint | ||
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| on: [push, pull_request] | ||
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| jobs: | ||
| lint: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/setup-python@v2 | ||
| - uses: psf/black@stable |
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| name: Test refgenie CLI | ||
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| on: | ||
| push: | ||
| branches: [master, dev] | ||
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| jobs: | ||
| test_CLI: | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| matrix: | ||
| python-version: [3.6, 3.8] | ||
| os: [ubuntu-latest, macos-latest] | ||
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| steps: | ||
| - uses: actions/checkout@v2 | ||
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| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: Install dev dependancies | ||
| run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi | ||
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| - name: Install package | ||
| run: python -m pip install . | ||
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| - name: install macOS-specific dependancies | ||
| if: startsWith(matrix.os, 'macOS') | ||
| run: brew install md5sha1sum | ||
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| - name: create genomes dir | ||
| run: mkdir genomes | ||
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| - name: refgenie init | ||
| working-directory: ./genomes | ||
| run: refgenie init -c g.yaml; cat g.yaml | ||
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| - name: refgenie list | ||
| working-directory: ./genomes | ||
| run: refgenie list -c g.yaml | ||
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| - name: refgenie build fasta (parent asset) | ||
| run: | | ||
| refgenie build -c genomes/g.yaml t7/fasta --files fasta=tests/data/t7.fa.gz --recipe tests/data/recipe_parent.json | ||
| ./tests/assert_in_file.sh genomes/g.yaml t7 0 | ||
| ./tests/assert_in_file.sh genomes/g.yaml 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905 0 # this is a digest that should be produced from this FASTA file | ||
| - name: refgenie build fasta_child (child asset) | ||
| run: | | ||
| refgenie build -c genomes/g.yaml t7/fasta_child --recipe tests/data/recipe_child.json | ||
| ./tests/assert_in_file.sh genomes/g.yaml fasta_child 0 | ||
| if [ -L `refgenie seek -c genomes/g.yaml t7/fasta_child` ]; then | ||
| echo "`refgenie seek -c genomes/g.yaml t7/fasta_child` exists." | ||
| else | ||
| echo "Error: `refgenie seek -c genomes/g.yaml t7/fasta_child` does not exist." | ||
| exit 1 | ||
| fi | ||
| if [ -d genomes/data/6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905/fasta_child/default ]; then | ||
| echo "'genomes/data/6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905/fasta_child/default' exists." | ||
| else | ||
| echo "Error: 'genomes/data/6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905/fasta_child/default' does not exist." | ||
| exit 1 | ||
| fi | ||
| - name: refgenie list | ||
| working-directory: ./genomes | ||
| run: refgenie list -c g.yaml | ||
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| - name: refgenie build fasta | ||
| run: refgenie build -c genomes/g.yaml t7/fasta --files fasta=tests/data/t7.fa.gz --recipe tests/data/recipe_parent.json | ||
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| - name: refgenie set aliases | ||
| run: | | ||
| refgenie alias set -c genomes/g.yaml --aliases t7_new t7_new1 --digest 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905 | ||
| ./tests/assert_in_file.sh genomes/g.yaml t7_new 0 | ||
| ./tests/assert_in_file.sh genomes/g.yaml t7_new1 0 | ||
| if [ -L `refgenie seek -c genomes/g.yaml t7_new/fasta` ]; then | ||
| echo "`refgenie seek -c genomes/g.yaml t7_new/fasta` exists." | ||
| else | ||
| echo "Error: `refgenie seek -c genomes/g.yaml t7_new/fasta` does not exist." | ||
| exit 1 | ||
| fi | ||
| if [ -L `refgenie seek -c genomes/g.yaml t7_new1/fasta` ]; then | ||
| echo "`refgenie seek -c genomes/g.yaml t7_new1/fasta` exists." | ||
| else | ||
| echo "Error: `refgenie seek -c genomes/g.yaml t7_new1/fasta` does not exist." | ||
| exit 1 | ||
| fi | ||
| - name: refgenie remove aliases | ||
| run: | | ||
| refgenie alias set -c genomes/g.yaml --aliases t7_another --digest 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905 | ||
| refgenie alias remove -c genomes/g.yaml --aliases t7_new t7_new1 t7 --digest 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905 | ||
| ./tests/assert_in_file.sh genomes/g.yaml t7_new 1 | ||
| ./tests/assert_in_file.sh genomes/g.yaml t7_new1 1 | ||
| ./tests/assert_in_file.sh genomes/g.yaml t7_another 0 | ||
| if [ -L genomes/alias/t7_new/fasta/default/6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905.fa.gz ]; then | ||
| echo "'genomes/alias/t7_new/fasta/default/6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905.fa.gz' exists." | ||
| exit 1 | ||
| else | ||
| echo "Error: 'genomes/alias/t7_new/fasta/default/6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905.fa.gz' does not exist." | ||
| fi | ||
| - name: refgenie get aliases | ||
| run: | | ||
| refgenie alias get -c genomes/g.yaml | ||
| - name: refgneie add asset | ||
| run: | | ||
| refgenie add t7_another/test_asset -c genomes/g.yaml --path ../tests/data --seek-keys '{"recipe": "recipe_parent.json"}' | ||
| ./tests/assert_in_file.sh genomes/g.yaml test_asset 0 | ||
| if [ -L `refgenie seek t7_another/test_asset.recipe:default -c genomes/g.yaml` ]; then | ||
| echo "`refgenie seek t7_another/test_asset.recipe:default -c genomes/g.yaml` exists." | ||
| else | ||
| echo "Error: `refgenie seek t7_another/test_asset.recipe:default -c genomes/g.yaml` does not exist." | ||
| exit 1 | ||
| fi | ||
| - name: refgenie tag asset | ||
| run: | | ||
| refgenie tag -c genomes/g.yaml t7_another/fasta_child:default -t new_tag -f | ||
| ./tests/assert_in_file.sh genomes/g.yaml new_tag 0 | ||
| if [ -f `refgenie seek t7_another/fasta_child:new_tag -c genomes/g.yaml` ]; then | ||
| echo "`refgenie seek t7_another/fasta_child:new_tag -c genomes/g.yaml` exists." | ||
| else | ||
| echo "Error: `refgenie seek t7_another/fasta_child:new_tag -c genomes/g.yaml` does not exist." | ||
| exit 1 | ||
| fi | ||
| - name: refgenie id | ||
| run: | | ||
| ./tests/assert_in_file.sh genomes/g.yaml `refgenie id -c genomes/g.yaml t7_another/fasta_child:new_tag` 0 | ||
| - name: refgenie remove fasta_child | ||
| run: | | ||
| refgenie remove -c genomes/g.yaml t7_another/fasta_child -f | ||
| ./tests/assert_in_file.sh genomes/g.yaml fasta_child 1 | ||
| ./tests/assert_in_file.sh genomes/g.yaml 6c5f19c9c2850e62cc3f89b04047fa05eee911662bd77905/fasta_child:new_tag 1 # test if the entry was removed from the fasta children list |
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@@ -80,3 +80,6 @@ refgenie.egg-info/ | |
| docs_jupyter/refgenie.yaml | ||
| docs_jupyter/rCRSd* | ||
| docs_jupyter/hs38d1* | ||
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| # build dir | ||
| build/ | ||
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