bitbucket-pipelines.yml

# This is a sample build configuration for Python.
# Check our guides at https://confluence.atlassian.com/x/x4UWN for more examples.
# Only use spaces to indent your .yml configuration.
# -----
# You can specify a custom docker image from Docker Hub as your build environment.
image: continuumio/miniconda3

options:
  docker: true

pipelines:
  default:
    - step:
        script: # Modify the commands below to build your repository.
          - apt-get update
          - apt-get install -y make gcc g++
          - conda install -c bioconda -c conda-forge -y mamba
          - mamba install -c bioconda -c conda-forge -y fastqc vispr snakemake cutadapt jinja2 numpy scipy
          # install the latest version of mageck
          - mkdir mageck
          - cd mageck
          - git clone https://davidliwei@bitbucket.org/liulab/mageck.git
          - cd mageck
          - python setup.py install
          - cd ../../
          #- python setup.py sdist
          - python setup.py install 
          #- step:
          #  script:
          - cd test/esc-testdata
          #- snakemake -F --cores 4
          - cd ../esc-testdata2-counttable
          - snakemake -F --cores 4
          - cd ../esc-testdata3-day0  
          - snakemake -F --cores 4
          - cd ../esc-testdata4-rra
          - snakemake -F --cores 4
    - step:
        script:
          # build the Docker image
          # - export IMAGE_NAME=davidliwei/mageck:$BITBUCKET_COMMIT
          - export IMAGE_NAME=davidliwei/mageck-vispr:latest
          - docker build -t $IMAGE_NAME .
          # authenticate with Docker Hub
          - docker login --username $DOCKER_HUB_USERNAME --password $DOCKER_HUB_PASSWORD 
          - docker push $IMAGE_NAME
          # build another image with current commit
          - export IMAGE_NAME=davidliwei/mageck-vispr:$BITBUCKET_COMMIT
          - docker build -t $IMAGE_NAME .
          - docker login --username $DOCKER_HUB_USERNAME --password $DOCKER_HUB_PASSWORD 
          - docker push $IMAGE_NAME