Setup Code

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#               Setup Terminal            #
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# 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 your_cyverse_username@your.atmosphere.ip.address

ssh grodriguez@128.196.142.26

# 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          #
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# 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


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#                   Importing Data                  #
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$ 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