.travis.yml

language: python
python: 2.7

git:
    submodules: false

before_install:
  - export GALAXY_REPO=https://github.com/galaxyproject/galaxy
  - export GALAXY_RELEASE=release_17.01
  - export PLANEMO_CONDA_PREFIX="$HOME/conda"
  - unset JAVA_HOME
  - git submodule init
  - git submodule update tools/one_snp_away

install:
  - pip install flake8 planemo==0.39
  - planemo conda_init
  - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"
  - conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools
  - . activate iuc_conda
  - planemo --version
  - conda --version
  - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$?
  - |
    if [ "$GIT_DIFF_EXIT_CODE" -gt 1 ] ; then
      git remote set-branches --add origin master;
      git fetch;
      TRAVIS_COMMIT_RANGE=origin/master...;
    fi
  - echo $TRAVIS_COMMIT_RANGE
  - |
      planemo ci_find_repos --exclude packages --exclude data_managers \
                            --changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \
                            --output changed_repositories_chunk.list
  - cat changed_repositories_chunk.list

script:
  - set -e
  - cd "$TRAVIS_BUILD_DIR" && flake8 --exclude=.git .
  - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR"; done < changed_repositories_chunk.list
  - while read -r DIR; do planemo conda_install "$DIR"; done < changed_repositories_chunk.list
  - while read -r DIR; do travis_wait 40 planemo test --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" "$DIR"; done < changed_repositories_chunk.list