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.travis.yml
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.travis.yml
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language: python
dist: trusty
sudo: true
python:
- 3.6
cache:
directories:
- $HOME/misc_cache
- $HOME/miniconda
env:
global:
- CACHE_DIR="$HOME/misc_cache"
- MINICONDA_DIR="$HOME/miniconda"
- GATK_PATH="$CACHE_DIR/GenomeAnalysisTK-3.6"
#- NOVOALIGN_PATH="$CACHE_DIR/bin_bundles/novocraft_v3"
- PYTHONIOENCODING=UTF8
# BUNDLE_SECRET for decrypting gatk tarball
- secure: 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
# ANACONDA_TOKEN anaconda.org token for user "broad-viral-ngs"
- secure: 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
# DOCKER_USER
- secure: 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
# DOCKER_PASS
- secure: 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
# DOCKER_EMAIL
- secure: 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
matrix:
- TEST_EASY_INSTALL=true
- TEST_EASY_INSTALL=long_prefix
- TEST_EASY_INSTALL=false
- TEST_EASY_INSTALL=git
matrix:
fast_finish: true
include:
- os: linux
dist: trusty
python: 2.7
sudo: required
services:
- docker
env:
- TEST_DOCKER=true
- TEST_EASY_INSTALL=false
addons:
apt:
packages:
- libffi-dev
- libssl-dev
# - os: osx
# language: generic
# env:
# - TRAVIS_OSX_PYTHON_VERSION=py35
# - TRAVIS_PYTHON_VERSION=3.5.1
git:
depth: 3
before_install:
- sudo apt-get update
- sudo apt-get -y -o Dpkg::Options::="--force-confnew" install docker-ce
- docker --version
- travis/before_install.sh
install:
- source travis/install-conda.sh
- source travis/install-licensed-tools.sh
- travis/install-licensed-tools.sh
- travis/install-pip.sh
script:
#- travis_wait 119 travis/tests-unit.sh
- travis/tests-unit.sh