Merge pull request #9 from d3b-center/rjcorb/docker-readme

add Dockerfile, update README

Dockerfile

@@ -0,0 +1,50 @@
+FROM rocker/tidyverse:4.4.0
+
+LABEL maintainer = "Ryan Corbett ([email protected])"
+
+
+#########################################
+RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
+
+# Add curl, bzip2 and some dev libs
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+    curl \
+    bzip2 \
+    zlib1g \
+    libbz2-dev \
+    liblzma-dev \
+    libreadline-dev
+
+# libmagick++-dev is needed for coloblindr to install
+RUN apt-get -y --no-install-recommends install \
+    libgdal-dev \
+    libudunits2-dev \
+    libmagick++-dev
+
+# Set the Bioconductor repository as the primary repository
+RUN R -e "options(repos = BiocManager::repositories())"
+
+# Install BiocManager and the desired version of Bioconductor
+RUN R -e "install.packages('BiocManager', dependencies=TRUE)"
+RUN R -e "BiocManager::install(version = '3.19')"
+
+# Install packages
+RUN R -e 'BiocManager::install(c( \
+  "circlize", \
+  "ComplexHeatmap", \
+  "data.table", \
+  "ggthemes", \
+  "readxl", \
+  "RColorBrewer", \
+  "survival", \
+  "survMisc", \
+  "survminer" \
+))'
+
+
+RUN R -e "remotes::install_github('clauswilke/colorblindr', ref = '1ac3d4d62dad047b68bb66c06cee927a4517d678', dependencies = TRUE)"
+RUN R -e "remotes::install_github('thomasp85/patchwork', ref = '1cb732b129ed6a65774796dc1f618558c7498b66')"
+
+WORKDIR /rocker-build/
+
+ADD Dockerfile . 

README.md

@@ -2,21 +2,26 @@
 
 This repository includes codes relevant to each radiomic analysis project.  
 
-### Badges
+### To reproduce the code in the `braf-fusions` module of this repository
 
-Update the LICENSE badge to point to the new repo location on GitHub.
-Note that the LICENSE badge will fail to render correctly unless the repo has
-been set to **public**.
+1. Clone the repository:
+```
+git clone [email protected]:d3b-center/TIRU_radiomic_analysis.git
+```
 
-Add additional badges for CI, docs, and other integrations as needed within the
-`<p>` tag next to the LICENSE.
+2. Pull Docker container:
+```
+docker pull pgc-images.sbgenomics.com/corbettr/tiru-radiomics:latest
+```
 
-### Repo Description
+3. Start the Docker container; from the `TIRU_radiomic_analysis` folder, run:
+```
+docker run --name <CONTAINER_NAME> -d -e PASSWORD=pass -p 8787:8787 -v $PWD:/home/rstudio/TIRU_radiomic_analysis pgc-images.sbgenomics.com/corbettr/tiru-radiomics:latest
+```
 
-Update the repositories description with a short summary of the repository's
-intent.
-Include an appropriate emoji at the start of the summary.
+NOTE: if using a Macbook with M1 chip, add the option `--platform linux/amd64` to above code
 
-Add a handful of tags that summarize topics relating to the repository.
-If the repo has a documentation site or webpage, add it next to the repository
-description.
+4. Execute the shell within the docker image; from the `TIRU_radiomic_analysis` folder, run: 
+```
+docker exec -ti <CONTAINER_NAME> bash
+```