update site development docker to newer Ruby

Author: obigriffith

README.md

@@ -20,8 +20,8 @@ The site should now be running on localhost port 4000. Changes to files will sho
 To install the site locally with docker run the following commands:
 
 1. Clone the repo `$ git clone git@github.com:griffithlab/rnabio.org.git`
-2. Pull the docker image `$ docker pull griffithlab/rnabiodev:0.0.4`
-3. Run the docker `$ docker run -p 4000:4000 -v ~/git/rnabio.org/:/opt/git/rnabio.org -it griffithlab/rnabiodev:0.0.4`
+2. Pull the docker image `$ docker pull griffithlab/rnabiodev:0.0.5`
+3. Run the docker `$ docker run -p 4000:4000 -v ~/git/rnabio.org/:/opt/git/rnabio.org -it griffithlab/rnabiodev:0.0.5`
 
 Make sure that the above command has correct path to cloned git repo (The first part specified with -v option). The site should now be running on localhost port 4000. Changes to files will show up interactively on localhost:4000.
 

docker/site/0.0.5/Dockerfile

@@ -0,0 +1,30 @@
+################################################################################
+##################### Set Inital Image to work from ############################
+
+FROM ruby:3.3.11
+
+################################################################################
+##################### Add Container Labels #####################################
+
+LABEL "Description"="ruby environment for development of rnabio.org site"
+
+################################################################################
+##################### Install Necessary gems ############################
+
+WORKDIR /tmp/rnabio.org
+RUN wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/Gemfile &&\
+    wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/Gemfile.lock &&\
+    wget https://raw.githubusercontent.com/griffithlab/rnabio.org/master/alembic-jekyll-theme.gemspec &&\
+    gem install bundler &&\
+    bundle install
+WORKDIR /usr/local/bin
+RUN echo "#!/bin/bash\nbundle exec jekyll serve --host 0.0.0.0 --watch" > start_jekyll.sh &&\
+    chmod +x start_jekyll.sh &&\
+    mkdir -p /opt/git/rnabio.org &&\
+    rm -rf /tmp/rnabio.org
+WORKDIR /opt/git/rnabio.org
+
+################################################################################
+##################### Set Entrypoint ############################
+ENTRYPOINT ["/usr/local/bin/start_jekyll.sh"]
+

docker/site/README

@@ -3,17 +3,17 @@
 
 #1. Create a new Dockerfile
 cd ~/git/rnabio.org/docker/site
-mkdir 0.0.2
-cd 0.0.2
-cp ~/git/rnabio.org/docker/site/0.0.1/Dockerfile .
+mkdir 0.0.5
+cd 0.0.5
+cp ~/git/rnabio.org/docker/site/0.0.4/Dockerfile .
 
 #2. Modify the new Dockerfile as needed
 
 #3. Make sure docker is running
 
 #4. Clean up docker environment
 #To ensure a clean/new build you may want to clean up (delete) old containers, images, volumes and cache
-#4.1 Deleted containers, images, and volumes directly in the docker desktop app
+#4.1 Delete containers, images, and volumes directly in the docker desktop app
 #4.2 Check for any remaining data in docker environment
 docker system df
 
@@ -22,11 +22,11 @@ docker buildx prune
 docker system df
 
 #Build a new image from modified Dockerfile
-docker build -t griffithlab/rnabiodev:0.0.2 ./
+docker build -t griffithlab/rnabiodev:0.0.5 ./
 
 #Test that the image is working
-docker run -p 4000:4000 -v ~/git/rnabio.org/:/opt/git/rnabio.org -it griffithlab/rnabiodev:0.0.2
+docker run -p 4000:4000 -v ~/git/rnabio.org/:/opt/git/rnabio.org -it griffithlab/rnabiodev:0.0.5
 
 #Once satistfied, push the image to dockerhub
-docker push griffithlab/rnabiodev:0.0.2
+docker push griffithlab/rnabiodev:0.0.5