diff --git a/DESCRIPTION b/DESCRIPTION index 4a86ea6a..d0f5e270 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,34 +1,28 @@ Package: sampleDB -Title: Organization for EPPIcenter Wetlab Samples -Version: 0.0.0.9000 -Authors@R: - person(given = "Severiano", - family = "Villarruel", - role = c("aut", "cre"), - email = "Severiano.Villarruel@ucsf.edu", - comment = c(ORCID = "YOUR-ORCID-ID")) -Description: Functions to imterface with EPPIcenter SampleDB database -Imports: +Title: A Management System for Wet Lab Samples +Version: 1.2.0 +Authors@R: c( + person("Severiano", "Villarruel", , "Severiano.Villarruel@ucsf.edu", role = c("aut", "cre")), + person("Brian", "Palmer", , "brian.palmer@ucsf.edu", role = c("aut", "ctb")) + ) +Description: SampleDB is a Management System for Wet Lab Samples. It can + be used to track a sample’s storage address and metadata. +License: MIT + file LICENSE +Encoding: UTF-8 +Language: es +Roxygen: TRUE +RoxygenNote: 7.2.1 +Imports: dplyr, - shiny, - RSQLite, - lubridate, - magrittr, emojifont, - fastmap, - shinyFeedback, - shinyWidgets, + lubridate, + markdown, purrr, + rappdirs, readr, - tidyr, - markdown, + RSQLite, + shinyFeedback, shinyjs, - DT, - rappdirs, - shinybusy -License: MIT + file LICENSE -Encoding: UTF-8 -LazyData: true -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.1 -URL: https://eppicenter.github.io/sampleDB-rpackage/ + shinyWidgets, + tidyr, + tools diff --git a/Dockerfile b/Dockerfile index d2710f10..4966eeaa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,28 +1,34 @@ -FROM rocker/shiny-verse:4.2.1 - -LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \ - org.opencontainers.image.source="https://github.com/rocker-org/rocker-versioned2" \ - org.opencontainers.image.vendor="Rocker Project" \ - org.opencontainers.image.authors="Carl Boettiger " - +FROM rocker/shiny:4.1.2 RUN apt-get update && apt-get install -y libpng-dev make zlib1g-dev && rm -rf /var/lib/apt/lists/* RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/ RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site RUN R -e 'install.packages("remotes")' +RUN Rscript -e 'remotes::install_version("purrr",upgrade="never", version = "0.3.4")' RUN Rscript -e 'remotes::install_version("rappdirs",upgrade="never", version = "0.3.3")' -RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.24")' +RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.0.10")' +RUN Rscript -e 'remotes::install_version("tidyr",upgrade="never", version = "1.2.1")' +RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.7.3")' RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")' +RUN Rscript -e 'remotes::install_version("shinyFeedback",upgrade="never", version = "0.4.0")' +RUN Rscript -e 'remotes::install_version("RSQLite",upgrade="never", version = "2.2.17")' +RUN Rscript -e 'remotes::install_version("readr",upgrade="never", version = "2.1.2")' RUN Rscript -e 'remotes::install_version("markdown",upgrade="never", version = "1.1")' -RUN Rscript -e 'remotes::install_version("emojifont",upgrade="never", version = "0.5.5")' RUN Rscript -e 'remotes::install_version("lubridate",upgrade="never", version = "1.8.0")' -RUN Rscript -e 'remotes::install_version("RSQLite",upgrade="never", version = "2.2.16")' +RUN Rscript -e 'remotes::install_version("emojifont",upgrade="never", version = "0.5.5")' +RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.24")' RUN mkdir /build_zone ADD . /build_zone WORKDIR /build_zone RUN R -e 'remotes::install_local(upgrade="never")' RUN rm -rf /build_zone -CMD R -e 'library(sampleDB)' -CMD R -e 'sampleDB::SampleDB_Setup()' +RUN R -e 'library(sampleDB); sampleDB::SampleDB_Setup();' +RUN << EOT bash + export SDB_PATH=$(R --slave -e "Sys.getenv('SDB_PATH')" | cut -f 2 -d " ") +EOT +VOLUME "$SDB_PATH" +RUN unset SDB_PATH EXPOSE 3838 + +CMD ["/usr/bin/shiny-server sampleDB"] \ No newline at end of file