Setup Code

Dockerfile

@@ -0,0 +1,21 @@
+FROM rocker/ropensci:latest
+FROM bioconductor/bioconductor_docker:devel
+
+RUN wget https://cran.r-project.org/src/contrib/Archive/nlme/nlme_3.1-123.tar.gz
+RUN R CMD INSTALL nlme_3.1-123.tar.gz
+
+RUN wget https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.2-17.tar.gz
+RUN R CMD INSTALL Matrix_1.2-17.tar.gz
+
+RUN install2.r openssl
+RUN install2.r swirl
+RUN install2.r --error \
+    hdf5r \
+    ## from bioconductor
+    && R -e "BiocManager::install('rhdf5', update=FALSE, ask=FALSE)"
+
+#Installs Qiime2 Package
+RUN installGithub.r jbisanz/qiime2R
+
+# To add data, create a seperate data.dat file in your working directory and run the line below without the '#'
+# ADD data.dat /home/rstudio/

Setup Code

@@ -0,0 +1,82 @@
+###########################################
+#               Setup Terminal            #
+###########################################
+
+# We need to connect to atomsphere.
+#   Note: You can you this program on you local computer but this allows for greater flexibility in computing power and memory.
+
+$ ssh [email protected]
+
+ssh [email protected]
+
+# If connecting for the first time, you may be get a security prompt.
+
+The authenticity of host '128.196.64.200 (128.196.64.200)' can\'t be established.
+ECDSA key fingerprint is SHA256:fzEJLqeljHgIwcGY0gUap2sRWLlGPQwUVimhEgkJYBs.
+Are you sure you want to continue connecting (yes/no)?
+
+# You may accept this prompt by typing 'yes'.
+# Enter Password
+
+# Establish Superuser 
+sudo su
+# Enter password when prompted, same as CyVerse Password.
+#   Note: This is needed to run the docker steps, otherwise you will need to include sudo in front of all your commands. 
+
+###########################################
+#          Getting Rocker set up          #
+###########################################
+# Install Docker
+snap install Docker
+
+#  This installs our R Studio with the base packages and more. 
+mkdir rocker-tutorial
+cd rocker-tutorial
+docker run rocker/ropensci
+
+#To terminate  the container hot Contrl C
+
+# We need to now install the packages for QIIME2
+# Using Nano or a code editor,  copy and paste/download the code from the file label "Dockerfile" into a new file called Dockerfile
+
+# Once you have the Dockerfile created, run this line to 
+docker build -t my-r-image .
+
+# This will take some time, so grab a coffe, go outside, and get some fresh air. There is another option!
+# Currently there exist an image and this is much faster to install
+# Pull Docker image 
+docker pull gbrodri/my-r-image:WorkingModel
+
+#To run the container
+docker run -dp 8787:8787 my-r-image
+# To access RStudio, you will enter your "Your IP address:8787" into the url of your browser. 
+#   Mind the fact the the url will be dependent on what machine your are running this on, local/virtual. 
+# Your username and password will both be rstudio
+
+# Once you are in, you can use RStudio like you normally would!
+
+#Follow the excellent tutorial by Jordan Bisanz 
+#https://forum.qiime2.org/t/tutorial-integrating-qiime2-and-r-for-data-visualization-and-analysis-using-qiime2r/4121
+
+
+#####################################################
+#                   Importing Data                  #
+#####################################################
+
+$ iinit
+
+# As prompted, enter the following values:
+# Host: data.cyverse.org
+# Port: 1247
+# User: your_cyverse_username
+# Zone: iplant
+# Password: your_cyverse_password
+
+# Testing Config for Data Store
+$ ils
+
+# To get a file Use
+$iget data_store_file
+
+# To upload from our instance to Data Store
+$iget file_on_instance location_on_data_store