Documentation and Docker updates

.dockerignore

@@ -1,3 +1,29 @@
-/shiny/*
 /vignettes/*
 /docs/*
+
+# ignore file extensions
+*.DS_Store
+*.Rmd
+*.html
+*.md
+*.Rhistory
+*.gitignore
+*.Rbuildignore
+*.Rproj
+DESCRIPTION
+
+# ignore folders
+**.git
+**.github
+**.Rproj.user
+*docs
+*vignettes
+*man
+*inst
+*pkgdown
+
+# ignore specific files
+docker-compose.yml
+docker-compose-*.yml
+_pkgdown.yml
+NAMESPACE

docker-compose.yaml

@@ -3,14 +3,19 @@ version: "3.9"
 x-data-volumes:
   &data-volume
   type: bind
-  source: $HOME/Github/Testings/seqsender
+  source: $HOME
   target: /data
 
 services:
-  seqsender: 
+  seqsender:
     container_name: seqsender
-    image: cdcgov/seqsender:latest
+    image: seqsender:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        - micromamba_version=1.5.3
     restart: always
-    volumes: 
+    volumes:
       - *data-volume
-    command: tail -f /dev/null 
+    command: tail -f /dev/null

shiny/app.py

@@ -163,20 +163,55 @@
                 ),
             ],
         ),
-        ui.nav_panel("Docker-Compose", "Panel A content"),
+        ui.nav_panel("Docker-Compose",
+            ui.h2("Update docker-compose.yaml for your local storage"),
+            ui.p(ui.strong("Note: "), ui.code("source"), " is the storage location of your local machine. This location will be mapped to ", ui.code("/data"), " directory inside of the container. Here we are mounting the local variable ", ui.code("$HOME"), " directory to ", ui.code("/data"), " inside of the container. Change the value ", ui.code("$HOME"), " to reflect your local storage system."),
+            ui.card(ui.HTML(
+                """
+<code>version: "3.9"<br>
+x-data-volumes:<br>
+&nbsp;&nbsp;&data-volume<br>
+&nbsp;&nbsp;type: bind<br>
+&nbsp;&nbsp;source: $HOME<br>
+&nbsp;&nbsp;target: /data<br>
+<br>
+services:<br>
+&nbsp;&nbsp;seqsender:<br>
+&nbsp;&nbsp;&nbsp;&nbsp;container_name: seqsender<br>
+&nbsp;&nbsp;&nbsp;&nbsp;image: seqsender:latest<br>
+&nbsp;&nbsp;&nbsp;&nbsp;build:<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;context: .<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dockerfile: Dockerfile<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;args:<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- micromamba_version=1.5.3<br>
+&nbsp;&nbsp;&nbsp;&nbsp;restart: always<br>
+&nbsp;&nbsp;&nbsp;&nbsp;volumes:<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- *data-volume<br>
+&nbsp;&nbsp;&nbsp;&nbsp;command: tail -f /dev/null<br>
+</code>"""
+                ),
+            style=terminal_css,
+            ),
+            ui.h2("Start ", ui.code("seqsender"), " container"),
+            ui.card(
+                ui.p(ui.code("docker-compose up -d")),
+            style=terminal_css,
+            ),
+            ui.p("Running docker-compose with the flag ", ui.code("-d"), " runs the container in detached mode, allowing the container to continue to run in the background. For more information refer to ", ui.a("docker-compose documentation", href="https://docs.docker.com/reference/cli/docker/compose/up/"), "."),
+        ),
         id="docker_options",
     ),
     ui.HTML(
         """
-<h2>check if the container is created successfully</h2>
+<h2>Check if the container is created successfully</h2>
 <pre><code>docker container ps</code></pre>
 """
     ),
     ui.card(
         ui.HTML(
             """
 docker container ps<br>
-CONTAINER ID&nbsp;|&nbsp;&nbsp;|&nbsp;IMAGE&nbsp;|&nbsp;&nbsp;|&nbsp;&nbsp;COMMAND&nbsp;|&nbsp;&nbsp;|&nbsp;CREATED&nbsp;|&nbsp;&nbsp;STATUS&nbsp;|&nbsp;PORTS&nbsp;|&nbsp;NAMES
+CONTAINER ID&nbsp;|&nbsp;&nbsp;|&nbsp;IMAGE&nbsp;|&nbsp;&nbsp;|&nbsp;&nbsp;COMMAND&nbsp;|&nbsp;&nbsp;|&nbsp;CREATED&nbsp;|&nbsp;&nbsp;STATUS&nbsp;|&nbsp;PORTS&nbsp;|&nbsp;NAMES<br>
 b37b6b19c4e8&nbsp;seqsender:latest&nbsp;&quot;/bin/bash&quot;&nbsp;5 hours ago&nbsp;Up 5 hours&nbsp;|&nbsp;&nbsp;|&nbsp;seqsender
 """
         ),