From 275c9052c17974bf0e3a2d3f9e90f7cd88fbe55a Mon Sep 17 00:00:00 2001 From: Gabriel Blake Rodriguez Date: Mon, 19 Apr 2021 09:42:09 -0400 Subject: [PATCH 1/6] Create Setup Code --- Setup Code | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 Setup Code diff --git a/Setup Code b/Setup Code new file mode 100644 index 0000000..ae6f12c --- /dev/null +++ b/Setup Code @@ -0,0 +1,70 @@ +# Setup +# We need to connect to atomsphere + +$ 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 + +# 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 + + +# 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. +# 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 +# Your username and password will both be rstudio + + From 3ff7558a62aae813460d5b19677fbfcb70a1a90a Mon Sep 17 00:00:00 2001 From: Gabriel Blake Rodriguez Date: Mon, 19 Apr 2021 09:45:04 -0400 Subject: [PATCH 2/6] Create Dockerfile --- Dockerfile | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..7a12b46 --- /dev/null +++ b/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/ From 0a53560cb08d8869e916eb524cb71e8e82ab4a10 Mon Sep 17 00:00:00 2001 From: Gabriel Blake Rodriguez Date: Mon, 19 Apr 2021 09:45:43 -0400 Subject: [PATCH 3/6] Update Setup Code --- Setup Code | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Setup Code b/Setup Code index ae6f12c..5e7d770 100644 --- a/Setup Code +++ b/Setup Code @@ -67,4 +67,7 @@ docker pull gbrodri/my-r-image:WorkingModel docker run -dp 8787:8787 my-r-image # Your username and password will both be rstudio +#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 + From 2a3b5d21067ab7aa144ca7c72e769bb0ecafbb74 Mon Sep 17 00:00:00 2001 From: Gabriel Blake Rodriguez Date: Mon, 19 Apr 2021 09:47:00 -0400 Subject: [PATCH 4/6] Update Setup Code --- Setup Code | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Setup Code b/Setup Code index 5e7d770..f6ba54c 100644 --- a/Setup Code +++ b/Setup Code @@ -58,8 +58,8 @@ docker run rocker/ropensci # 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. -# Currently there exist an. image and this is much faster to install +# 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 From 57ade968f27e24c23ca15064a920b3cb3406be50 Mon Sep 17 00:00:00 2001 From: Gabriel Blake Rodriguez Date: Mon, 19 Apr 2021 09:53:53 -0400 Subject: [PATCH 5/6] Update Setup Code --- Setup Code | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Setup Code b/Setup Code index f6ba54c..9c5a07a 100644 --- a/Setup Code +++ b/Setup Code @@ -65,8 +65,12 @@ 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 From f9f3cd8e3e20a5160c6b6e80d187be5aab161909 Mon Sep 17 00:00:00 2001 From: Gabriel Blake Rodriguez Date: Mon, 19 Apr 2021 10:29:58 -0400 Subject: [PATCH 6/6] Update Setup Code --- Setup Code | 67 +++++++++++++++++++++++++++++------------------------- 1 file changed, 36 insertions(+), 31 deletions(-) diff --git a/Setup Code b/Setup Code index 9c5a07a..e902680 100644 --- a/Setup Code +++ b/Setup Code @@ -1,51 +1,35 @@ -# Setup -# We need to connect to atomsphere +########################################### +# 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 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 +# 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 - +# You may accept this prompt by typing 'yes'. # Enter Password -#Establish Superuser +# Establish Superuser sudo su -#Enter password when prompted - -# 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 - - -# Getting Rocker set up +# 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 +# This installs our R Studio with the base packages and more. mkdir rocker-tutorial cd rocker-tutorial docker run rocker/ropensci @@ -75,3 +59,24 @@ docker run -dp 8787:8787 my-r-image #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