Merge pull request #55 from omnideconv/alex_dev

Updated Version of Webserver for DeconvExplorer
omnideconv · Feb 27, 2024 · 583b813 · 583b813
2 parents ec0d8f1 + 0315bf0
commit 583b813
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Showing 9 changed files with 18 additions and 26 deletions.
diff --git a/inst/webserver_setup/app/CIBERSORT.R → .../deconvexplorer-webserver/app/CIBERSORT.R b/inst/webserver_setup/app/CIBERSORT.R → .../deconvexplorer-webserver/app/CIBERSORT.R
diff --git a/inst/webserver_setup/app/Dockerfile → inst/deconvexplorer-webserver/app/Dockerfile b/inst/webserver_setup/app/Dockerfile → inst/deconvexplorer-webserver/app/Dockerfile
@@ -6,10 +6,10 @@ FROM rocker/r-base
 ARG GITHUB_PAT
 
 RUN apt-get update && apt-get install -y \
+    binutils \
     sudo \
     pandoc \
     apt-utils \
-    #pandoc-citeproc \
     libcurl4-gnutls-dev \
     libcairo2-dev \
     libxt-dev \
@@ -27,13 +27,12 @@ RUN apt-get update && apt-get install -y \
 # omnideconv and DeconvExplorer
 #RUN install2.r --error textshaping
 
-RUN install2.r --error pak car matlib 
-#RUN R -e "remotes::install_github('omnideconv/omnideconv', dependencies=TRUE)"
-RUN R -e "pak::pkg_install('omnideconv/omnideconv', dependencies=TRUE)"
-#RUN R -e "remotes::install_github('omnideconv/DeconvExplorer', dependencies=TRUE)"
+RUN install2.r --error pak car matlib remotes
+RUN R -e "remotes::install_github('omnideconv/omnideconv', dependencies=TRUE)"
 RUN R -e "pak::pkg_install('omnideconv/DeconvExplorer', dependencies=TRUE)"
 
-RUN R -e "reticulate::install_miniconda(force=TRUE)" # will not install automatically
+#RUN R -e "reticulate::install_miniconda()" # will not install automatically
+
 
 RUN R -e "omnideconv::install_all_python()"
 
@@ -56,9 +55,7 @@ COPY /*.R /srv/shiny-server/
 #RUN chmod -R +r /srv/shiny-server
 RUN chown -R shiny:shiny /srv/shiny-server
 
-
 EXPOSE 3838
 
-
 CMD ["R", "-e", "shiny::runApp('/srv/shiny-server/', host = '0.0.0.0', port = 3838)"]
 #CMD ["/usr/bin/shiny-server.sh"]
diff --git a/inst/webserver_setup/app/app.R → inst/deconvexplorer-webserver/app/app.R b/inst/webserver_setup/app/app.R → inst/deconvexplorer-webserver/app/app.R
diff --git a/inst/webserver_setup/app/shiny-server.conf → ...vexplorer-webserver/app/shiny-server.conf b/inst/webserver_setup/app/shiny-server.conf → ...vexplorer-webserver/app/shiny-server.conf
diff --git a/inst/webserver_setup/app/shiny-server.sh → ...onvexplorer-webserver/app/shiny-server.sh b/inst/webserver_setup/app/shiny-server.sh → ...onvexplorer-webserver/app/shiny-server.sh
diff --git a/inst/webserver_setup/docker-compose.yml → ...convexplorer-webserver/docker-compose.yml b/inst/webserver_setup/docker-compose.yml → ...convexplorer-webserver/docker-compose.yml
@@ -1,38 +1,33 @@
 version: "3.5"
 
 services:
-  deconvexplorer:
-    build:
-      context: ./app
-      args:
-        GITHUB_PAT: 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
-    image: deconv_explorer:latest
-    expose:
-      - 3838
-    networks:
-      - sp-net-deconvexplorer
   shinyproxy:
     build: ./shinyproxy
-    depends_on:
-      - deconvexplorer
     expose:
       - 8080
     networks:
-      - sp-net-deconvexplorer
+      sp-net:
+        ipv4_address: 172.16.199.3
     volumes:
       - /var/run/docker.sock:/var/run/docker.sock
       - ./logs/:/opt/shinyproxy/container-logs/
   nginx:
     image: nginx:1.17.5
     restart: unless-stopped
     ports:
-      - 3828:80
+      - 3868:80
     networks:
-      - sp-net-deconvexplorer
+      sp-net:
+        ipv4_address: 172.16.199.4
     depends_on:
       - shinyproxy
     volumes:
       - ./nginx/nginx.conf:/etc/nginx/nginx.conf
 
 networks:
-  sp-net-deconvexplorer:
+  sp-net:
+    driver: bridge
+    ipam:
+      driver: default
+      config:
+        - subnet: 172.16.199.0/24
diff --git a/inst/webserver_setup/nginx/nginx.conf → ...deconvexplorer-webserver/nginx/nginx.conf b/inst/webserver_setup/nginx/nginx.conf → ...deconvexplorer-webserver/nginx/nginx.conf
diff --git a/inst/webserver_setup/shinyproxy/Dockerfile → ...vexplorer-webserver/shinyproxy/Dockerfile b/inst/webserver_setup/shinyproxy/Dockerfile → ...vexplorer-webserver/shinyproxy/Dockerfile
diff --git a/...ebserver_setup/shinyproxy/application.yml → ...orer-webserver/shinyproxy/application.yml b/...ebserver_setup/shinyproxy/application.yml → ...orer-webserver/shinyproxy/application.yml
@@ -25,8 +25,8 @@ proxy:
           "-e",
           "shiny::runApp('/srv/shiny-server/', host = '0.0.0.0', port = 3838)",
         ]
-      container-network: webserversetup_sp-net-deconvexplorer
-      container-image: deconv_explorer:latest
+      container-network: deconvexplorer-webserver_sp-net
+      container-image: alexd13/deconv_explorer:1.0
       #container-cpu-limit: 2
 
 logging: