LodSeq/.gitlab-ci.yml at master · CNRGH/LodSeq · GitHub

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stages:
    - prepare
    - build
    - test

image: centos:7.4.1708

variables:
    CI_IMAGE: registry.cnrgh.fr/jmercier/LodSeq/ci:1.0.0-0
    DOCKER_DRIVER: overlay2


.build_snakemake: &build_snakemake
    stage: build
    script:
        - export  LANG=en_US.UTF-8
        -  yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm https://centos7.iuscommunity.org/ius-release.rpm
        - yum update -y
        - yum install -y curl python36u python36u-devel python36u-setuptools python36u-pip bzip2 gcc bc
        - curl -LO https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
        - bash Miniconda2-latest-Linux-x86_64.sh -b -p /usr/local/miniconda
        - export PATH=/usr/local/miniconda/bin:$PATH
        - conda update conda
        - conda install pip
        - pip3.6 install --upgrade pip
        - pip3.6 install wrapt requests ratelimiter pyyaml configargparse appdirs datrie jsonschema docutils jinja2
        - snakemake_version=${CI_JOB_NAME/*-}
        - curl -Lo snakemake-${snakemake_version}.tar.bz2 https://bitbucket.org/snakemake/snakemake/get/v${snakemake_version}.tar.bz2
        - mkdir snakemake && tar xf snakemake-${snakemake_version}.tar.bz2 -C snakemake --strip-components=1
        - pushd snakemake
        - python3.6 setup.py install
        - popd
        - conda env create -n lodseq --file environment.yaml

build snakemake-5.1.2: *build_snakemake
build snakemake-4.8.0: *build_snakemake

.test_genetic_data: &test_genetic_data
    stage: test
    script:
        - export  LANG=en_US.UTF-8
        - yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm https://centos7.iuscommunity.org/ius-release.rpm
        - yum update -y
        - yum install -y curl python36u python36u-devel python36u-setuptools python36u-pip bzip2 gcc bc
        - curl -LO https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
        - bash Miniconda2-latest-Linux-x86_64.sh -b -p /usr/local/miniconda
        - export PATH=/usr/local/miniconda/bin:$PATH
        - conda update conda
        - conda install pip
        - pip3.6 install --upgrade pip
        - pip3.6 install wrapt requests ratelimiter pyyaml configargparse appdirs datrie jsonschema docutils jinja2
        - snakemake_version=${CI_JOB_NAME/*-}
        - curl -Lo snakemake-${snakemake_version}.tar.bz2 https://bitbucket.org/snakemake/snakemake/get/v${snakemake_version}.tar.bz2
        - mkdir snakemake && tar xf snakemake-${snakemake_version}.tar.bz2 -C snakemake --strip-components=1
        - pushd snakemake
        - python3.6 setup.py install
        - popd
        - conda env create -n lodseq --file environment.yaml
        - curl -LO ftp://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz
        - mkdir -p data/inputs/genetic_map_HapMapII_GRCh37
        - tar xf genetic_map_HapMapII_GRCh37.tar.gz -C data/inputs/genetic_map_HapMapII_GRCh37
        - source activate lodseq
        - mkdir test/
        - snakemake --ignore-incomplete --reason --verbose --printshellcmds --timestamp  --configfile config.yaml
        - tar xf data/outputs/mergeResults.tar.gz -C data/outputs/
        - for f in $(ls test/mergeResults/results_*); do diff -q test/mergeResults/${f##*/} data/outputs/mergeResults/${f##*/}; done

test genetic data with snakemake-5.1.2: *test_genetic_data
test genetic data with snakemake-4.8.0: *test_genetic_data