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Commit479fdeb

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Merge pull request#314 from bcgsc/release/v3.0.0
Release/v3.0.0
2 parentse4c67a5 +c2221fe commit479fdeb

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‎.github/CONTRIBUTING.md

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##Getting Started
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If you are new to the project a good way to get started is by adding to the documentation, or adding unit tests where
@@ -47,7 +46,6 @@ mkdocs build
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The contents of the user manual can then be viewed by opening the build-docs/index.html
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in any available web browser (i.e. google-chrome, firefox, etc.)
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##Deploy to PyPi
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Install deployment dependencies
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twine upload -r pypi dist/*
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```
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##Reporting a Bug
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Please make sure to search through the issues before reporting a bug to ensure there isn't
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already an open issue.
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##Conventions
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###Linting
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Use[black](https://github.com/psf/black) with strings off and line length 100
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```bash
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black mavis -S -l 100
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blacksrc/mavis -S -l 100
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```
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###Docstrings
@@ -112,7 +108,6 @@ def some_function(some_arg: List[str]) -> None:
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any column name which may appear in any of the intermediate or final output files must be defined in`mavis.constants.COLUMNS` as well as added to the[columns glossary](../outputs/columns)
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###Tests
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- all new code must have unit tests in the tests subdirectory

‎.github/workflows/build.yml

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name:build
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on:[push, pull_request]
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on:
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push:
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branches:
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-master
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-develop
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pull_request:
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jobs:
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build:
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runs-on:ubuntu-latest
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strategy:
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matrix:
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python-version:[3.6, 3.7, 3.8]
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python-version:["3.7", "3.8", "3.9", "3.10"]
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name:python-${{ matrix.python-version }}
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steps:
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-uses:actions/checkout@v2
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-name:install machine dependencies
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python-version:${{ matrix.python-version }}
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-name:Install dependencies
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run:|
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python -m pip install --upgrade pip "setuptools<58" wheel
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pip install .[test]
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-name:Lint with flake8
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run:|
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 mavis --count --select=E9,F63,F7,F82 --show-source --statistics
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-name:Lint with black
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run:|
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pip install black
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# stop the build if black needs to be run
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black mavis -S -l 100 --check
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python -m pip install --upgrade pip setuptools
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pip install -e .[test] # need editable to make sure the coverage reports correctly
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-name:install bwa
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run:|
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git clone https://github.com/lh3/bwa.git
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run:|
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wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
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chmod a+x blat
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-name:run short tests with pytest
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-name:set up .pth file
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run:|
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export PATH=$PATH:$(pwd):$(pwd)/bwa
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pytest tests -v --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov mavis --cov-report term --cov-report xml --durations=10
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env:
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RUN_FULL:0
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if:github.event_name != 'pull_request'
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python tests/setup_subprocess_cov.py
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-name:run full tests with pytest
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run:|
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export PATH=$PATH:$(pwd):$(pwd)/bwa
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pytest tests -v --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov mavis --cov-report term --cov-report xml --durations=10
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export COVERAGE_PROCESS_START=$(pwd)/.coveragerc
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pytest tests -v \
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--junitxml=junit/test-results-${{ matrix.python-version }}.xml \
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--cov mavis \
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--cov tools.convert_annotations_format \
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--cov-report term-missing \
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--cov-report xml \
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--durations=10 \
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--cov-branch
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env:
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RUN_FULL:1
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if:github.event_name == 'pull_request'
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-name:Upload pytest test results
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uses:actions/upload-artifact@master
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with:
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name:codecov-umbrella
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fail_ci_if_error:true
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if:matrix.python-version == 3.8
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docker:
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runs-on:ubuntu-latest
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name:docker build
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steps:
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-uses:actions/checkout@v2
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-name:build the docker container
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run:|
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docker build --file Dockerfile --tag bcgsc/mavis:latest .
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-name:test the help menu
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run:|
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docker run bcgsc/mavis -h
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-name:Set up Python 3.7
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uses:actions/setup-python@v2
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with:
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python-version:3.7
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-name:Install workflow dependencies
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run:|
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python -m pip install --upgrade pip setuptools wheel
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pip install mavis_config pandas snakemake
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-uses:eWaterCycle/setup-singularity@v6
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with:
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singularity-version:3.6.4
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-name:docker2singularity
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run:
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docker run --mount type=bind,source=/var/run/docker.sock,target=/var/run/docker.sock --mount type=bind,source="$(pwd)",target=/output --privileged -t --rm singularityware/docker2singularity bcgsc/mavis:latest
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-name:Run analysis with snakemake & singularity
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run:|
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# get the SIMG filename
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export SNAKEMAKE_CONTAINER=$(ls *mavis*.simg)
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snakemake -j 2 --configfile tests/mini-tutorial.config.json --use-singularity
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if:always()

‎.github/workflows/publish.yml

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types:[created]
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jobs:
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deploy:
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pypi:
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runs-on:ubuntu-latest
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steps:
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-uses:actions/checkout@v2
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-name:Set up Python
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python setup.py sdist bdist_wheel install
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twine check dist/*
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twine upload dist/*
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docker:
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runs-on:ubuntu-latest
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steps:
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-uses:actions/checkout@v2
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-run:docker login -u $DOCKER_USER -p $DOCKER_PASSWORD
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env:
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DOCKER_USER:${{ secrets.DOCKER_USER }}
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DOCKER_PASSWORD:${{ secrets.DOCKER_PASSWORD }}
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-run:|
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docker build --file Dockerfile --tag bcgsc/mavis:latest --tag bcgsc/mavis:${{ github.event.release.tag_name }} .
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-run:docker push bcgsc/mavis:latest
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-run:docker push bcgsc/mavis:${{ github.event.release.tag_name }}

‎.github/workflows/quick-tests.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name:quick-tests
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on:[push]
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jobs:
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build:
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runs-on:ubuntu-latest
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strategy:
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matrix:
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python-version:["3.7", "3.8", "3.9", "3.10"]
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name:python-${{ matrix.python-version }} quick
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steps:
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-uses:actions/checkout@v2
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-name:Set up Python ${{ matrix.python-version }}
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uses:actions/setup-python@v2
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with:
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python-version:${{ matrix.python-version }}
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-name:Install dependencies
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run:|
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python -m pip install --upgrade pip setuptools wheel
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pip install .[test]
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-name:Lint with flake8
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run:|
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 src/mavis --count --select=E9,F63,F7,F82 --show-source --statistics
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-name:Lint with black
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run:|
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pip install black
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# stop the build if black needs to be run
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black src/mavis -S -l 100 --check
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-name:install bwa
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run:|
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git clone https://github.com/lh3/bwa.git
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cd bwa
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git checkout v0.7.17
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make
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cd ..
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-name:install blat
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run:|
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wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
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chmod a+x blat
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-name:run short tests with pytest
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run:|
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export PATH=$PATH:$(pwd):$(pwd)/bwa
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pytest tests -v \
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--junitxml=junit/test-results-${{ matrix.python-version }}.xml \
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--durations=10
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env:
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RUN_FULL:0

‎.gitignore

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# python generated files
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/.eggs
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/coverage
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/venv
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/venv*
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/.coverage
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*.pyc
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*__pycache__
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.tox
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*eggs/
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.mypy_cache
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.snakemake
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# aligners
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blat
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/docs/package/mavis/*/*.md
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# don't ignore subpackage summary files
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!/docs/package/mavis/*/index.md
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docs/configuration/settings.md
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.snakemake
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output_dir*
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bin
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dag*
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tutorial_data
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reference_inputs
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tmp

‎.readthedocs.yml

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-method:pip
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path:.
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extra_requirements:
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-docs
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-doc

‎Dockerfile

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FROM python:3.7-slim-buster
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WORKDIR /app
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RUN apt-get update && \
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apt-get upgrade -y && \
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apt-get install -y git wget make gcc libz-dev
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# pysam dependencies
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RUN apt-get install -y libncurses5-dev zlib1g-dev libbz2-dev libncursesw5-dev liblzma-dev
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# install BWA
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RUN git clone https://github.com/lh3/bwa.git && \
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cd bwa && \
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git checkout v0.7.17 && \
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make && \
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cd .. && \
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mv bwa/bwa /usr/local/bin
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# install minimap2
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RUN git clone https://github.com/lh3/minimap2.git && \
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cd minimap2 && \
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git checkout v2.24 && \
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make && \
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cd .. && \
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mv minimap2/minimap2.1 /usr/local/bin
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# install blat dependencies
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RUN apt-get install -y libcurl4
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# install blat
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RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat && \
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chmod a+x blat && \
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mv blat /usr/local/bin
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# install wtdbg2
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RUN git clone https://github.com/ruanjue/wtdbg2.git && \
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cd wtdbg2 && \
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make && \
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cd .. && \
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mv wtdbg2/wtdbg2 /usr/local/bin
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COPY setup.py setup.py
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COPY setup.cfg setup.cfg
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COPY MANIFEST.in MANIFEST.in
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COPY pyproject.toml pyproject.toml
47+
COPY src src
48+
COPY LICENSE LICENSE
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COPY README.md README.md
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# install python package
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RUN pip install -U setuptools pip wheel
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RUN pip install .
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RUN which mavis
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ENTRYPOINT ["mavis" ]

‎MANIFEST.in

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recursive-include docs *
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recursive-include tests *.py
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include tests/*/data/*
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recursive-include mavis *.py
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recursive-include tools *.pl *.py *.pm
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recursive-include tab *.py
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recursive-include src *.py *.json
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include src/mavis/py.typed
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include README.md
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include LICENSE
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prune docs/build
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prunedocs/source/auto
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prune docs
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prunetests

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