Dockerize

Author: ppernot

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

R/packages.R

@@ -18,15 +18,16 @@
 # }
 # # ## Other libraries ----
 # devtools::install_github("ppernot/ErrViewLib")
-# library(lib,character.only = TRUE)
 
 # Cloud deployment ----
 
 library("devtools")
 library("shiny")
+library("shinythemes")
 library("shinyFiles")
 library("shinyAce")
 library("shinycssloaders")
+library("DT")
 library("boot")
 library("ErrViewLib")
 library("data.table")

compressDB.sh

@@ -0,0 +1 @@
+tar -cvzf ChemDB.tar.gz ../MC-ChemDB/Neutrals/Source/v_1.3 

docker/Dockerfile

@@ -0,0 +1,42 @@
+FROM ppernot1/shiny_base
+
+RUN apt-get install -y --no-install-recommends libharfbuzz-dev libfribidi-dev
+
+## renv
+ENV RENV_VERSION 0.15.5
+RUN Rscript -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN Rscript -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
+
+RUN mkdir MC-ChemDBUI
+COPY .Rprofile /MC-ChemDBUI/
+COPY renv/activate.R /MC-ChemDBUI/renv/activate.R
+COPY renv.lock /MC-ChemDBUI/renv.lock
+WORKDIR /MC-ChemDBUI
+RUN R -e 'renv::consent(TRUE)' \
+ && R -e 'renv::restore()'
+
+## database files
+WORKDIR /
+RUN mkdir ChemDBPublic
+ADD ChemDB.tar.gz /
+
+## app files
+COPY global.R /MC-ChemDBUI/
+COPY ui.R /MC-ChemDBUI/
+COPY server.R /MC-ChemDBUI/
+COPY ui_files /MC-ChemDBUI/ui_files/
+COPY server_files /MC-ChemDBUI/server_files/
+COPY R /MC-ChemDBUI/R/
+COPY data /MC-ChemDBUI/data/
+WORKDIR /MC-ChemDBUI
+
+
+## change user from root ### BREAKS renv links !!!
+#RUN addgroup --system app \
+#    && adduser --system --ingroup app app
+#RUN chown app:app -R /UncVal
+#USER app
+
+## expose port and run app
+EXPOSE 3820
+CMD ["R", "-e", "shiny::runApp(host = '0.0.0.0', port = 3820)"]

docker/commands.txt

@@ -0,0 +1,13 @@
+BUILD :
+    1/ cd MC-ChemDBUI
+    2/ docker build -t ppernot1/mc-chemdbui:v0.1 -t ppernot1/mc-chemdbui:latest -f docker/Dockerfile .
+    3/ docker login
+    4/ docker image push --all-tags ppernot1/mc-chemdbui
+
+RUN :
+   UI :
+       1/ docker run -d -p 3820:3820 --mount type=bind,source="$(pwd)"/../ChemDBPublic,target=/ChemDBPublic --name mc-chemdbui ppernot1/mc-chemdbui
+       3/ access http://localhost:3820 in browser
+
+   BASH :
+       * docker run -ti ppernot1/mc-chemdbui bash

global.R

@@ -27,7 +27,7 @@ gPars$mar[3] = 2
 
 # Data paths ####
 neutralsSource = file.path('..','MC-ChemDB','Neutrals','Source')
-neutralsPublic = file.path('.','ChemDBPublic','Neutrals')
+neutralsPublic = file.path('..','ChemDBPublic','Neutrals')
 
 # Load data and functions ####
 source('R/massCalc.R')