From 8475c00bd695ea7f9739a92525dbdfb66a458213 Mon Sep 17 00:00:00 2001
From: Michael Geuenich <m.geuenich@mail.utoronto.ca>
Date: Thu, 1 Jun 2023 21:50:14 -0700
Subject: [PATCH] add docker resources

---
 Dockerfile                   | 17 +++++++++++++++++
 scripts/install_R_packages.R | 30 ++++++++++++++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 scripts/install_R_packages.R

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..2c9a28b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,17 @@
+FROM bioconductor/bioconductor_docker:RELEASE_3_16-R-4.2.3
+
+ADD scripts/install_R_packages.R /tmp/install_R_packages.R
+RUN Rscript /tmp/install_R_packages.R
+
+# Install Python 3
+RUN apt-get update && apt-get install -y python3
+
+# Install pip for Python 3
+RUN apt-get install -y python3-pip
+
+# Install Python packages
+RUN pip3 install numpy pandas sklearn joblib
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+RUN git clone --depth 1 https://github.com/tidyverse/ggplot2.git
diff --git a/scripts/install_R_packages.R b/scripts/install_R_packages.R
new file mode 100644
index 0000000..a92e59d
--- /dev/null
+++ b/scripts/install_R_packages.R
@@ -0,0 +1,30 @@
+packages <- c(
+    'tidyverse',
+    'RColorBrewer',
+    'patchwork',
+    'caret',
+    'SingleCellExperiment',
+    'splitstackshape',
+    'fabricatr',
+    'scmap',
+    'SingleR',
+    'Seurat',
+    'yaml',
+    'glue',
+    'scater',
+    'yardstick',
+    'data.table',
+    'scales',
+    'ComplexHeatmap',
+    'circlize',
+    'viridis',
+    'ggalluvial',
+    'magick',
+    'ggpubr',
+    'broom'
+)
+
+ip <- installed.packages()
+packages <- packages[!(packages %in% rownames(ip))]
+
+BiocManager::install(packages)
\ No newline at end of file