From a526b41cfa29d91c99dfce317d2d863329e78a97 Mon Sep 17 00:00:00 2001
From: gfinak <greg.finak@gmail.com>
Date: Wed, 11 Jul 2018 15:51:04 -0700
Subject: [PATCH] Add Dockerfile and Makefile for building docker container of
 opencyto flow tools. Update buildignore

---
 .Rbuildignore |  2 ++
 Dockerfile    | 34 ++++++++++++++++++++++++++++++++++
 Makefile      |  5 +++++
 3 files changed, 41 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 Makefile

diff --git a/.Rbuildignore b/.Rbuildignore
index 21c47f67..783f316e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 sticker.R
 inst/figures
+Dockerfile
+Makefile
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..fba1a1cb
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,34 @@
+FROM rocker/rstudio:latest
+
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+  libxml2-dev \
+  libcairo2-dev \
+  libsqlite3-dev \
+  libmariadbd-dev \
+  libmariadb-client-lgpl-dev \
+  libpq-dev \
+  libssh2-1-dev \
+  unixodbc-dev \
+  libgeos-dev \
+  libudunits2-dev \
+  libgdal-dev
+RUN R -e "install.packages(c('rgeos','sf','units'),type='source')" 
+RUN R -e "source('https://bioconductor.org/biocLite.R')" \
+  && install2.r --error \
+    --deps TRUE \
+    tidyverse \
+    dplyr \
+    ggplot2 \
+    devtools \
+    formatR \
+    remotes \
+    selectr \
+    caTools \
+  && R -e "library(BiocInstaller); biocLite(c('openCyto','COMPASS','MIMOSA','CytoML','ggcyto'))" 
+# not clear why selectr needs explicit re-install, see https://github.com/rocker-org/rocker-versioned/pull/63
+
+## Notes: Above install2.r uses --deps TRUE to get Suggests dependencies as well,
+## dplyr and ggplot are already part of tidyverse, but listed explicitly to get their (many) suggested dependencies.
+## In addition to the the title 'tidyverse' packages, devtools is included for package development.
+## RStudio wants formatR for rmarkdown, even though it's not suggested.
+## remotes included for installation from heterogenous sources including git/svn, local, url, and specific cran versions
diff --git a/Makefile b/Makefile
new file mode 100644
index 00000000..564473c7
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,5 @@
+latest:
+	docker build -t gfinak/opencyto .
+
+
+