From 635b784fba87d0c6757ead908a106aa738be3086 Mon Sep 17 00:00:00 2001
From: "Hylke C. Donker" <hylke.donker@gmail.com>
Date: Thu, 17 Feb 2022 11:50:55 +0100
Subject: [PATCH] Added example snippets of the presentation.

---
 Dockerfile                                | 19 +++++++++++++++++++
 example/example.R                         |  4 ++++
 example/test/test_linear_transformation.R | 12 ++++++++++++
 readme.md                                 | 12 ++++++++++++
 4 files changed, 47 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 example/example.R
 create mode 100644 example/test/test_linear_transformation.R
 create mode 100644 readme.md

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..75cd9f4
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,19 @@
+FROM r-base:4.1.2
+
+# Install several CRAN packages using package manager.
+RUN apt update \
+    && apt install --assume-yes \
+    r-cran-dplyr=1.0.7-2 \
+    r-bioc-deseq2=1.34.0+dfsg-1 \
+    r-cran-biocmanager=1.30.16+dfsg-3 \
+    r-cran-devtools=2.4.3-1
+
+# Example how to install specific package using R.
+RUN R -e "BiocManager::install('apeglm', dependencies=TRUE, version='3.14')"
+
+# Make a directory in the Docker image and copy scripts to it.
+WORKDIR /analysis/
+COPY ./example/ /analysis/
+
+# Run unit tests.
+CMD R --quiet -e 'testthat::test_dir("test")'
\ No newline at end of file
diff --git a/example/example.R b/example/example.R
new file mode 100644
index 0000000..51221df
--- /dev/null
+++ b/example/example.R
@@ -0,0 +1,4 @@
+# Example function to be tested.
+linear_transformation <- function(x) {
+    return (2*x + 1)
+}
\ No newline at end of file
diff --git a/example/test/test_linear_transformation.R b/example/test/test_linear_transformation.R
new file mode 100644
index 0000000..f6e5348
--- /dev/null
+++ b/example/test/test_linear_transformation.R
@@ -0,0 +1,12 @@
+source("../example.R", chdir=TRUE)
+library(testthat)
+
+test_that("Real numbers are transformed to odd numbers.", {
+  expect_equal(linear_transformation(3) %% 2, 1)
+  expect_equal(linear_transformation(4) %% 2, 1)
+})
+
+test_that("Positive numbers remain positive.", {
+  expect_true(linear_transformation(3) > 0)
+  expect_true(linear_transformation(10) > 0)
+})
diff --git a/readme.md b/readme.md
new file mode 100644
index 0000000..d79fcbb
--- /dev/null
+++ b/readme.md
@@ -0,0 +1,12 @@
+# Snippets of the `Reproducible and error free scripts` presentation
+Use the `Dockerfile` to build the image, which we name `r_example`:
+
+```Bash
+docker build -t r_example .
+```
+
+As specified in the image's Dockerfile (`CMD` line), by default it will run the unit tests:
+
+```Bash
+docker run r_example
+```