diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3db98cb342edae8203a658be61fe0231be23923e..184484902e6d1975d861358a3d8f6b5dd0e05d9b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,7 +1,21 @@ image: kontrapunkt/eci test: - script: + stage: test + variables: + METFRAG_JAR: "/usr/local/bin/MetFragCommandLine-2.5.0.jar" + script: - R CMD build . --no-build-vignettes --no-manual - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual - R -e 'devtools::test()' + + +build: + stage: build + only: + - master + - devel + script: + - echo "Hello $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG" + + diff --git a/docker/shinyscreen.Dockerfile b/docker/shinyscreen.Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..eafba10df8547c439e4e64ca468d5d40b0561e9a --- /dev/null +++ b/docker/shinyscreen.Dockerfile @@ -0,0 +1 @@ +FROM kontrapunkt/eci diff --git a/docker/testenv.Dockerfile b/docker/testenv.Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..2c8d9f0862ec671955cf4e8a42d94da08afcb371 --- /dev/null +++ b/docker/testenv.Dockerfile @@ -0,0 +1,37 @@ +FROM ubuntu:jammy-20230126 + + +RUN apt-get update +RUN apt-get install -y --no-install-recommends apt-utils r-base r-recommended g++ gfortran +RUN apt-get install -y --no-install-recommends curl libxml2-dev libssl-dev libssh2-1-dev zlib1g-dev +RUN apt-get install -y --no-install-recommends xdg-utils automake autoconf gcc make pkg-config +RUN apt-get install -y --no-install-recommends net-tools git-all default-jre-headless zlib1g zlib1g-dev +RUN apt-get install -y --no-install-recommends libnetcdf* openbabel libhdf5-1* libhdf5-hl-1* +RUN apt-get install -y --no-install-recommends r-cran-rcolorbrewer r-cran-data.table r-cran-biocmanager r-cran-tidyverse r-cran-cowplot +RUN apt-get install -y --no-install-recommends r-cran-curl r-cran-promises r-cran-yaml +RUN apt-get install -y --no-install-recommends r-cran-dt r-cran-future +RUN apt-get install -y --no-install-recommends r-cran-rjava r-cran-rsvg r-cran-png +RUN apt-get install -y --no-install-recommends r-cran-rmarkdown r-cran-shiny r-cran-htmltools +RUN apt-get install -y --no-install-recommends r-cran-rcdklibs r-cran-rcdk r-cran-fingerprint +RUN apt-get install -y --no-install-recommends r-bioc-affy r-bioc-affyio +RUN apt-get install -y --no-install-recommends r-cran-devtools +RUN apt-get install -y --no-install-recommends libpng16-16 libpng-tools libpng-dev libpng++-dev +RUN rm -rf /var/lib/apt/lists/* +RUN rm -rf /tmp/* + + +RUN R -e 'install.packages("enviPat", dependencies=TRUE)' +RUN R -e 'BiocManager::install(c("Rhdf5lib","mzR","MSnbase","RMassBank"),update=F)' +RUN R -e 'devtools::install_git("https://github.com/CDK-R/rinchi", dependencies=F)' +RUN R -e 'devtools::install_git("https://github.com/schymane/RChemMass", dependencies=F)' +#R -e 'devtools::install_git("https://github.com/CDK-R/rcdklibs", dependencies=F)' +#R -e 'devtools::install_git("https://github.com/CDK-R/cdkr", subdir="rcdk", dependencies=F)' + +# Add MetFrag +RUN curl -LJO https://github.com/ipb-halle/MetFragRelaunched/releases/download/v.2.5.0/MetFragCommandLine-2.5.0.jar + +RUN cp MetFragCommandLine-2.5.0.jar /usr/local/bin +RUN chmod 0777 /usr/local/bin/MetFragCommandLine-2.5.0.jar + + +