Revision a3646bba2173e34fae60f533c832db516da3cbd1 authored by Alexey Sergushichev on 25 April 2019, 14:44:44 UTC, committed by Alexey Sergushichev on 25 April 2019, 14:44:44 UTC
1 parent 5eb3dbd
.travis.yml
language: r
r:
#- bioc-devel
- bioc-release
# warnings_are_errors: true
sudo: false
fortran: true
cache: packages
services:
- docker
addons:
apt:
packages:
- libprotobuf-dev
- libapparmor-dev
- protobuf-compiler
- libcurl4-openssl-dev
r_packages:
- covr
- data.table
- ggplot2
- testthat
- knitr
- rmarkdown
- httpuv
- opencpu
- protolite
- Rook
- unix
os:
- linux
- osx
bioc_required: true
bioc_packages:
- BiocCheck
- GEOquery
- limma
- rhdf5
- BiocStyle
before_install:
- if [ ${TRAVIS_OS_NAME} = 'osx' ]; then brew unlink python; brew install protobuf; fi
- R -e 'install.packages("devtools")'
- R -e 'source("https://bioconductor.org/biocLite.R"); biocLite()'
- R -e 'devtools::install_github("ctlab/fgsea", tag="1.9.4")'
script:
- R CMD build .
- FILE=$(ls -1t *.tar.gz | head -n 1)
- R CMD check "$FILE"
- bash inst/test_js.sh
after_script:
- FILE=$(ls -1t *.tar.gz | head -n 1)
- Rscript -e "library(BiocCheck); BiocCheck(\"${FILE}\")"
after_success:
- Rscript -e 'covr::codecov()'
notifications:
slack:
rooms:
- sysbio1:Kt2QCRqnbzJpNE8TvOvgwEMz#phantasus
jobs:
include:
- stage: Docker build
env: DOCKER_TAG="$TRAVIS_BRANCH-$TRAVIS_BUILD_NUMBER"
language: minimal
before_install: skip
after_script: skip
after_success: skip
r_packages: skip
install: skip
script: if [ "$TRAVIS_OS_NAME" == "linux" ] && [ "$TRAVIS_BRANCH" == "master" ]; then
docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
docker build -t dzenkova/phantasus --build-arg PHANTASUS_BUILD=$DOCKER_TAG --build-arg GITHUB_PAT=$GITHUB_PAT . ;
docker tag dzenkova/phantasus dzenkova/phantasus:$DOCKER_TAG ;
docker push dzenkova/phantasus;
fi
- stage: Docker build
env: DOCKER_TAG="$TRAVIS_BRANCH-$TRAVIS_BUILD_NUMBER"
language: minimal
before_install: skip
after_script: skip
after_success: skip
r_packages: skip
install: skip
script: if [ "$TRAVIS_OS_NAME" == "linux" ] && [ "$TRAVIS_BRANCH" == "develop" ]; then
docker login -u="$DOCKER_USERNAME" -p="$DOCKER_PASSWORD";
docker build --build-arg PHANTASUS_BUILD=$DOCKER_TAG --build-arg GITHUB_PAT=$GITHUB_PAT -t dzenkova/phantasus:develop . ;
docker tag dzenkova/phantasus:develop dzenkova/phantasus:$DOCKER_TAG ;
docker push dzenkova/phantasus:develop;
docker push dzenkova/phantasus:$DOCKER_TAG;
fi
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