first commit

3.5.0/Dockerfile

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+FROM rocker/verse:3.5.0
+MAINTAINER "Tyson Lee Swetnam [email protected]"
+# This image uses the Rocker verse RStudio image - thanks R OpenSci!
+
+# Add additional R libraries beyond Rocker verse which fit our specific project needs.
+RUN install2.r --error \    
+    # Added Packages
+    PerformanceAnalytics \
+    boot \
+    devtools \
+    dlm \
+    dplyr \
+    foreign \
+    lubridate \
+    plotly \
+    truncreg \
+    ggridges 
+
+## Install CyVerse VICE Depends
+RUN apt-get update && apt-get install -y lsb wget apt-transport-https python2.7 python-requests curl supervisor nginx gnupg2
+
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - \
+    && echo "deb [arch=amd64] https://packages.irods.org/apt/ xenial main" > /etc/apt/sources.list.d/renci-irods.list \
+    && apt-get update \
+	&& apt-get install -y irods-icommands
+
+ADD https://github.com/hairyhenderson/gomplate/releases/download/v2.5.0/gomplate_linux-amd64 /usr/bin/gomplate
+RUN chmod a+x /usr/bin/gomplate
+
+# provide read and write access to Rstudio users for default R library location
+RUN chmod -R 777 /usr/local/lib/R/site-library
+
+ENV PASSWORD "rstudio1"
+RUN bash /etc/cont-init.d/userconf
+
+COPY run.sh /usr/local/bin/run.sh
+RUN chmod +x /usr/local/bin/run.sh
+
+COPY nginx.conf.tmpl /nginx.conf.tmpl
+COPY rserver.conf /etc/rstudio/rserver.conf
+COPY supervisor-nginx.conf /etc/supervisor/conf.d/nginx.conf
+COPY supervisor-rstudio.conf /etc/supervisor/conf.d/rstudio.conf
+
+ENV REDIRECT_URL "http://localhost/"
+
+ENTRYPOINT ["/usr/local/bin/run.sh"]

3.5.0/README.md

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+v3.5.0

3.5.0/nginx.conf.tmpl

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+daemon off;
+worker_processes  1;
+
+error_log  /var/log/nginx/error.log warn;
+pid        /var/run/nginx.pid;
+
+
+events {
+    worker_connections  1024;
+}
+
+
+http {
+
+  map $http_upgrade $connection_upgrade {
+      default upgrade;
+      ''      close;
+    }
+
+  server {
+    listen 80;
+
+    location / {
+      proxy_pass http://localhost:8787;
+      proxy_redirect http://localhost:8787 {{.Env.REDIRECT_URL}};
+      proxy_http_version 1.1;
+      proxy_set_header Upgrade $http_upgrade;
+      proxy_set_header Connection $connection_upgrade;
+      proxy_read_timeout 20d;
+    }
+  }
+}

3.5.0/rserver.conf

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+# Server Configuration File
+
+www-address=127.0.0.1
+rsession-which-r=/usr/local/bin/R

3.5.0/run.sh

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+#!/bin/sh
+
+gomplate -f /nginx.conf.tmpl -o /etc/nginx/nginx.conf
+supervisord -c /etc/supervisor/supervisord.conf -n

3.5.0/supervisor-nginx.conf

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+[program:nginx]
+command=nginx

3.5.0/supervisor-rstudio.conf

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+[program:rstudio]
+command=/usr/lib/rstudio-server/bin/rserver --server-daemonize 0

3.5.1/Dockerfile

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+FROM rocker/verse:3.5.1
+MAINTAINER "Tyson Lee Swetnam [email protected]"
+# This image uses the Rocker verse RStudio image - thanks R OpenSci!
+
+# Add additional R libraries beyond Rocker verse which fit our specific project needs.
+RUN install2.r --error \    
+    # Added Packages
+    PerformanceAnalytics \
+    boot \
+    devtools \
+    dlm \
+    dplyr \
+    foreign \
+    lubridate \
+    plotly \
+    truncreg \
+    ggridges 
+
+## Install CyVerse VICE Depends
+RUN apt-get update && apt-get install -y lsb wget apt-transport-https python2.7 python-requests curl supervisor nginx gnupg2
+
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - \
+    && echo "deb [arch=amd64] https://packages.irods.org/apt/ xenial main" > /etc/apt/sources.list.d/renci-irods.list \
+    && apt-get update \
+	&& apt-get install -y irods-icommands
+
+ADD https://github.com/hairyhenderson/gomplate/releases/download/v2.5.0/gomplate_linux-amd64 /usr/bin/gomplate
+RUN chmod a+x /usr/bin/gomplate
+
+# provide read and write access to Rstudio users for default R library location
+RUN chmod -R 777 /usr/local/lib/R/site-library
+
+ENV PASSWORD "rstudio1"
+RUN bash /etc/cont-init.d/userconf
+
+COPY run.sh /usr/local/bin/run.sh
+RUN chmod +x /usr/local/bin/run.sh
+
+COPY nginx.conf.tmpl /nginx.conf.tmpl
+COPY rserver.conf /etc/rstudio/rserver.conf
+COPY supervisor-nginx.conf /etc/supervisor/conf.d/nginx.conf
+COPY supervisor-rstudio.conf /etc/supervisor/conf.d/rstudio.conf
+
+ENV REDIRECT_URL "http://localhost/"
+
+ENTRYPOINT ["/usr/local/bin/run.sh"]

3.5.1/README.md

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+v3.5.1

3.5.1/nginx.conf.tmpl

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+daemon off;
+worker_processes  1;
+
+error_log  /var/log/nginx/error.log warn;
+pid        /var/run/nginx.pid;
+
+
+events {
+    worker_connections  1024;
+}
+
+
+http {
+
+  map $http_upgrade $connection_upgrade {
+      default upgrade;
+      ''      close;
+    }
+
+  server {
+    listen 80;
+
+    location / {
+      proxy_pass http://localhost:8787;
+      proxy_redirect http://localhost:8787 {{.Env.REDIRECT_URL}};
+      proxy_http_version 1.1;
+      proxy_set_header Upgrade $http_upgrade;
+      proxy_set_header Connection $connection_upgrade;
+      proxy_read_timeout 20d;
+    }
+  }
+}

3.5.1/rserver.conf

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+# Server Configuration File
+
+www-address=127.0.0.1
+rsession-which-r=/usr/local/bin/R

3.5.1/run.sh

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+#!/bin/sh
+
+gomplate -f /nginx.conf.tmpl -o /etc/nginx/nginx.conf
+supervisord -c /etc/supervisor/supervisord.conf -n

3.5.1/supervisor-nginx.conf

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+[program:nginx]
+command=nginx

3.5.1/supervisor-rstudio.conf

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+[program:rstudio]
+command=/usr/lib/rstudio-server/bin/rserver --server-daemonize 0

3.5.2/Dockerfile

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+yFROM rocker/verse:3.5.2
+MAINTAINER "Tyson Lee Swetnam [email protected]"
+# This image uses the Rocker verse RStudio image - thanks R OpenSci!
+
+# Add additional R libraries beyond Rocker verse which fit our specific project needs.
+RUN install2.r --error \    
+    # Added Packages
+    PerformanceAnalytics \
+    boot \
+    devtools \
+    dlm \
+    dplyr \
+    foreign \
+    lubridate \
+    plotly \
+    truncreg \
+    ggridges 
+
+## Install CyVerse VICE Depends
+RUN apt-get update && apt-get install -y lsb wget apt-transport-https python2.7 python-requests curl supervisor nginx gnupg2
+
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - \
+    && echo "deb [arch=amd64] https://packages.irods.org/apt/ xenial main" > /etc/apt/sources.list.d/renci-irods.list \
+    && apt-get update \
+	&& apt-get install -y irods-icommands
+
+ADD https://github.com/hairyhenderson/gomplate/releases/download/v2.5.0/gomplate_linux-amd64 /usr/bin/gomplate
+RUN chmod a+x /usr/bin/gomplate
+
+# provide read and write access to Rstudio users for default R library location
+RUN chmod -R 777 /usr/local/lib/R/site-library
+
+ENV PASSWORD "rstudio1"
+RUN bash /etc/cont-init.d/userconf
+
+COPY run.sh /usr/local/bin/run.sh
+RUN chmod +x /usr/local/bin/run.sh
+
+COPY nginx.conf.tmpl /nginx.conf.tmpl
+COPY rserver.conf /etc/rstudio/rserver.conf
+COPY supervisor-nginx.conf /etc/supervisor/conf.d/nginx.conf
+COPY supervisor-rstudio.conf /etc/supervisor/conf.d/rstudio.conf
+
+ENV REDIRECT_URL "http://localhost/"
+
+ENTRYPOINT ["/usr/local/bin/run.sh"]

3.5.2/README.md

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+v3.5.2

3.5.2/nginx.conf.tmpl

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+daemon off;
+worker_processes  1;
+
+error_log  /var/log/nginx/error.log warn;
+pid        /var/run/nginx.pid;
+
+
+events {
+    worker_connections  1024;
+}
+
+
+http {
+
+  map $http_upgrade $connection_upgrade {
+      default upgrade;
+      ''      close;
+    }
+
+  server {
+    listen 80;
+
+    location / {
+      proxy_pass http://localhost:8787;
+      proxy_redirect http://localhost:8787 {{.Env.REDIRECT_URL}};
+      proxy_http_version 1.1;
+      proxy_set_header Upgrade $http_upgrade;
+      proxy_set_header Connection $connection_upgrade;
+      proxy_read_timeout 20d;
+    }
+  }
+}

3.5.2/rserver.conf

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+# Server Configuration File
+
+www-address=127.0.0.1
+rsession-which-r=/usr/local/bin/R

3.5.2/run.sh

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+#!/bin/sh
+
+gomplate -f /nginx.conf.tmpl -o /etc/nginx/nginx.conf
+supervisord -c /etc/supervisor/supervisord.conf -n

3.5.2/supervisor-nginx.conf

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+[program:nginx]
+command=nginx

3.5.2/supervisor-rstudio.conf

@@ -0,0 +1,2 @@
+[program:rstudio]
+command=/usr/lib/rstudio-server/bin/rserver --server-daemonize 0

3.5.3/Dockerfile

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+FROM rocker/verse:3.5.3
+MAINTAINER "Tyson Lee Swetnam [email protected]"
+# This image uses the Rocker verse RStudio image - thanks R OpenSci!
+
+# Add additional R libraries beyond Rocker verse which fit our specific project needs.
+RUN install2.r --error \    
+    # Added Packages
+    PerformanceAnalytics \
+    boot \
+    devtools \
+    dlm \
+    dplyr \
+    foreign \
+    lubridate \
+    plotly \
+    truncreg \
+    ggridges 
+
+USER root
+# Install CyVerse VICE Depends
+RUN apt-get update && apt-get install -y lsb wget apt-transport-https python2.7 python-requests curl supervisor nginx gnupg2
+
+# install iCommands
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - \
+    && echo "deb [arch=amd64] https://packages.irods.org/apt/ bionic main" > /etc/apt/sources.list.d/renci-irods.list \
+    && apt-get update \
+    && apt-get install -y irods-icommands \
+    && apt-get clean \
+    && rm -rf /usr/lib/apt/lists/* 
+
+ADD https://github.com/hairyhenderson/gomplate/releases/download/v2.5.0/gomplate_linux-amd64 /usr/bin/gomplate
+RUN chmod a+x /usr/bin/gomplate
+
+# provide read and write access to Rstudio users for default R library location
+RUN chmod -R 777 /usr/local/lib/R/site-library
+
+ENV PASSWORD "rstudio1"
+RUN bash /etc/cont-init.d/userconf
+
+COPY run.sh /usr/local/bin/run.sh
+RUN chmod +x /usr/local/bin/run.sh
+
+COPY nginx.conf.tmpl /nginx.conf.tmpl
+COPY rserver.conf /etc/rstudio/rserver.conf
+COPY supervisor-nginx.conf /etc/supervisor/conf.d/nginx.conf
+COPY supervisor-rstudio.conf /etc/supervisor/conf.d/rstudio.conf
+
+ENV REDIRECT_URL "http://localhost/"
+
+ENTRYPOINT ["/usr/local/bin/run.sh"]

3.5.3/README.md

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+v3.5.3

3.5.3/nginx.conf.tmpl

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+daemon off;
+worker_processes  1;
+
+error_log  /var/log/nginx/error.log warn;
+pid        /var/run/nginx.pid;
+
+
+events {
+    worker_connections  1024;
+}
+
+
+http {
+
+  map $http_upgrade $connection_upgrade {
+      default upgrade;
+      ''      close;
+    }
+
+  server {
+    listen 80;
+
+    location / {
+      proxy_pass http://localhost:8787;
+      proxy_redirect http://localhost:8787 {{.Env.REDIRECT_URL}};
+      proxy_http_version 1.1;
+      proxy_set_header Upgrade $http_upgrade;
+      proxy_set_header Connection $connection_upgrade;
+      proxy_read_timeout 20d;
+    }
+  }
+}

3.5.3/rserver.conf

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+# Server Configuration File
+
+www-address=127.0.0.1
+rsession-which-r=/usr/local/bin/R

3.5.3/run.sh

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+#!/bin/sh
+
+gomplate -f /nginx.conf.tmpl -o /etc/nginx/nginx.conf
+supervisord -c /etc/supervisor/supervisord.conf -n

3.5.3/supervisor-nginx.conf

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+[program:nginx]
+command=nginx

3.5.3/supervisor-rstudio.conf

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+[program:rstudio]
+command=/usr/lib/rstudio-server/bin/rserver --server-daemonize 0