Merge pull request #71 from ipb-halle/feature/cleanup-and-refactor

Feature/cleanup and refactor

Dockerfile

@@ -4,10 +4,10 @@ MAINTAINER Kristian Peters <[email protected]>
 
 LABEL Description="MetFamily helps identifying metabolites and groups them into metabolite clusters (a.k.a. families)."
 
-WORKDIR /srv/shiny-server
-
-RUN rm -rf *
-
-ADD MetFamily /srv/shiny-server/
+ADD . /tmp/MetFamily
 
+RUN R CMD INSTALL /tmp/MetFamily
 
+WORKDIR /srv/shiny-server
+RUN rm -rf *
+ADD inst/MetFamily /srv/shiny-server/

Dockerfile-base

@@ -1,19 +1,30 @@
+# syntax=docker/dockerfile:1.3-labs
 FROM rocker/shiny:3.6.3
 
 MAINTAINER Kristian Peters <[email protected]>
 
 LABEL Description="MetFamily Base Image with dependencies."
 
-RUN apt-get -y update && apt-get -y install \
+RUN apt-get -y --allow-releaseinfo-change update && apt-get -y install \
   netcdf-bin libnetcdf-dev libdigest-sha-perl libigraph0-dev \
-  xorg-dev libglu1-mesa-dev freeglut3-dev libgomp1 libxml2-dev gcc g++ libcurl4-gnutls-dev libssl-dev gdebi-core
+  xorg-dev libglu1-mesa-dev freeglut3-dev libgomp1 libxml2-dev gcc g++ libcurl4-gnutls-dev libssl-dev gdebi-core libharfbuzz-dev libfribidi-dev libtiff5-dev
 
 ENV NETCDF_INCLUDE=/usr/include
 RUN echo 'sanitize_errors off;disable_protocols xdr-streaming xhr-streaming iframe-eventsource iframe-htmlfile;' >> /etc/shiny-server/shiny-server.conf
 
-ADD binder /tmp
-RUN R -e "source('/tmp/install.R')"
+COPY <<EOF /root/.Rprofile
+local({
+  r <- getOption(\"repos\")
+  r[\"CRAN\"] <- \"https://packagemanager.posit.co/cran/2020-04-23/\"
+  options(repos=r)
+})
+EOF
+
+ADD DESCRIPTION /tmp/MetFamily/DESCRIPTION
+RUN R -e 'options(warn=2) ; install.packages("devtools")'
+RUN R -e 'options(warn=2) ; install.packages("XML")'
+RUN R -e 'options(warn=2) ; install.packages("MALDIquant")'
+RUN R -e 'options(warn=2) ; install.packages("FactoMineR")'
+RUN R -e 'library(devtools); options(warn=2) ; install_deps("/tmp/MetFamily")'
 
 WORKDIR /srv/shiny-server
-
-

README.md

@@ -34,6 +34,14 @@ of `rstudio:rstudio`. Do not use in Production !
 You can also pass a local directory with checked out MetFamily git tree 
 via the `docker run -v` argument.
 
+## Running locally with MetFamily R Package
+
+After installing the `MetFamily` R package and its dependencies, you can 
+```
+library(MetFamily)
+runApp(system.file("MetFamily", package="MetFamily"))
+```
+
 ## Running through Kubernetes
 
 At IPB we are running MetFamily inside a Kubernetes cluster. 

binder/install.R

@@ -1,39 +1,43 @@
 
 install.packages("devtools")
-library("devtools")
 install.packages("BiocManager")
 
-install.packages("shiny")
-install.packages("testthat")
-
-devtools::install_github("rstudio/htmltools")
-devtools::install_github("decisionpatterns/searchable")
-
-install.packages("shinyjs")
-install.packages("shinybusy")
-install.packages("DT")
-install.packages("colourpicker")
-install.packages("shinyBS")
-install.packages("egg")
-install.packages("cowplot")
-install.packages("searchable")
-install.packages("gdata")
+library("devtools")
+devtools::install_deps("..")
 
-BiocManager::install("mzR")
-BiocManager::install("xcms")
-BiocManager::install("mixOmics")
-BiocManager::install("pcaMethods")
 
-install.packages("FactoMineR")
-install.packages("matrixStats")
-install.packages("Matrix")
-install.packages("stringi")
-install.packages("slam")
-install.packages("knitr")
-install.packages("cba")
-install.packages("squash")
-install.packages("plotrix")
-install.packages("RColorBrewer")
-install.packages("plotly")
-install.packages("rlang")
+# install.packages("shiny")
+# install.packages("testthat")
+# 
+# devtools::install_github("rstudio/htmltools")
+# devtools::install_github("decisionpatterns/searchable")
+# 
+# install.packages("shinyjs")
+# install.packages("shinybusy")
+# install.packages("DT")
+# install.packages("colourpicker")
+# install.packages("shinyBS")
+# install.packages("egg")
+# install.packages("cowplot")
+# install.packages("searchable")
+# install.packages("gdata")
+# 
+# BiocManager::install("mzR")
+# BiocManager::install("xcms")
+# BiocManager::install("mixOmics")
+# BiocManager::install("pcaMethods")
+# 
+# install.packages("car")
+# install.packages("FactoMineR")
+# install.packages("matrixStats")
+# install.packages("Matrix")
+# install.packages("stringi")
+# install.packages("slam")
+# install.packages("knitr")
+# install.packages("cba")
+# install.packages("squash")
+# install.packages("plotrix")
+# install.packages("RColorBrewer")
+# install.packages("plotly")
+# install.packages("rlang")