View source for Docker Applications

= Homelab =
* [[Self_hosting|Self hosting]]
* [https://noted.lol/what-are-your-most-used-self-hosted-applications What are your Most Used Self Hosted Applications?] and [https://www.reddit.com/r/selfhosted/comments/udxlnp/what_are_your_most_used_self_hosted_applications/ more]
* [https://youtu.be/9uF2us2PabM?si=ia76EPobqVRohIOy Best Docker Containers for Home Server!] 2022/11 (video)

== Top/best ==
* https://hub.docker.com/
* [https://github.com/veggiemonk/awesome-docker Awesome Docker]
* [https://fleet.linuxserver.io/ LinuxServer.io]. Need to sort by downloads.
* Reddit [https://www.reddit.com/r/homelab/comments/zy5io8/what_are_your_must_docker_containers_for_home_lab/ what are your must docker containers for home lab?]
* [https://www.blackvoid.club/docker-top-10-images-and-solutions/ Docker top (18) images and solutions]
* [https://www.smarthomebeginner.com/best-docker-containers-for-home-server/ 60+ Best Docker Containers for Home Server Beginners 2023]

= Templates =
* [https://github.com/Lissy93/portainer-templates 400+ 1-click Portainer app templates]

= App store =
== Tipi ==
* [https://github.com/meienberger/runtipi Tipi — A personal homeserver for everyone]
* [https://www.reddit.com/r/selfhosted/comments/vbl4aq/tipi_version_030_released/ Tipi version 0.3.0 released]

= Dockerizing Compiled Software =
* https://ram.tianon.xyz/post/2017/12/26/dockerize-compiled-software.html
* [https://www.howtogeek.com/devops/how-to-containerize-a-legacy-application/ How to Containerize a Legacy Application]

= Crontab =
* [https://www.howtogeek.com/devops/how-to-use-cron-with-your-docker-containers/ How to Use Cron With Your Docker Containers]
* [https://github.com/alseambusher/crontab-ui Crontab UI]

= Install macOS =
* [https://www.linuxuprising.com/2021/03/install-macos-big-sur-or-catalina-in.html Install macOS Big Sur Or Catalina In A Virtual Machine Using Docker-OSX]
* [https://youtu.be/BOyZ6g7penE This is Real!! MacOS Docker] 2022/12/2
* [https://www.makeuseof.com/create-macos-virtual-machine-using-docker/ How to Create a macOS Virtual Machine Using Docker]

= Raspberry Pi servers based on Docker =
* https://github.com/pi-hosted/pi-hosted
* [https://youtu.be/a6mjt8tWUws Raspberry Pi Server based on Docker, with VPN, Dropbox backup, Influx, Grafana, etc.]

= Data Science =
[[Data_science#Container|Data Science]]

= Illumina BaseSpace =
* http://blog.basespace.illumina.com/2013/10/21/introducing-the-native-app-engine/
* https://developer.basespace.illumina.com/docs/content/documentation/getting-started/overview
* https://developer.basespace.illumina.com/docs/content/documentation/native-apps/manage-docker-image

= Bioinformatics analyses =
<ul>
<li>[https://www.biorxiv.org/content/early/2017/10/17/204495 Hot-starting software containers for bioinformatics analyses]
<li>[https://academic.oup.com/gigascience/article/6/8/1/3894236 Bio-Docklets: virtualization containers for single-step execution of NGS pipelines]
<li>[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009244 Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources] Hanussek, 2021
<li>[https://github.com/StaPH-B/docker-builds docker-builds] - Dockerfiles and documentation on tools for public health bioinformatics
<li>[https://github.com/shmohammadi86/ACTIONet/tree/R-release/mini_docker ACTIONet] and the paper [https://pubmed.ncbi.nlm.nih.gov/36650127/ Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington's disease] 2023.
<li>[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05695-9 CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications] 2024

[[File:CredoError.png|240px]]
</ul>

= Cloud provider =
Docker can be deployed on any cloud provider like Digital Ocean, Amazon Web Services (AWS), Microsoft Azure, Google Cloud Computing.

* https://www.digitalocean.com/community/tutorials/how-to-use-the-digitalocean-docker-application
* http://go.mkb.io/post/118463195802/docker-machine-with-digital-ocean
* http://networkstatic.net/running-docker-machine-on-digital-ocean/
* http://linoxide.com/linux-how-to/use-docker-machine-cloud-provider/
* [http://www.ithome.com.tw/news/106274 HTC採用AWS的三大原因]: 上市時間縮短、節省成本以及提供創新發想的低成本空間。

= Dashboard =
[https://www.howtogeek.com/homelab-dashboard-what-it-is-and-why-you-need-one/ Homelab Dashboard: What It Is and Why You Need One]

== Dashy ==
* https://github.com/Lissy93/dashy
* [https://youtu.be/QsQUzutGarA Dashy, a configurable, themable, flexible personal dashboard for your homelab!] (video) and [https://wiki.opensourceisawesome.com/books/self-hosted-dashboards/page/dashy-powerful-informative-configurable-self-hosting-dashboard Notes]
** https://github.com/walkxcode/dashboard-icons for icons
* Icons are located in ~/dash/icons/dashboard-icons/png directory.
* Download an icon from [https://icons8.com/icons/ icons8.com] or [https://uxwing.com/ uxwing.com]. The default 48x48 works fine.
* Better to work on one icon and then save the change. Repeat.
<pre>
docker run -d \
  -p 8295:80 \
  --volume /home/$USER/dashy/public/conf.yml:/app/public/conf.yml \
  --volume /home/$USER/dashy/icons:/app/public/item-icons/icons \
  --name dashy \
  --restart=unless-stopped \
  lissy93/dashy:latest
</pre>

== Glance ==
* https://github.com/glanceapp/glance
* [https://www.youtube.com/watch?v=2dGD4C2g8ig Glance Dashboard: Your New Favorite Docker Dashboard]
== Homepage ==
<ul>
<li>https://github.com/gethomepage/homepage
* [https://gethomepage.dev/configs/ Documentation]
* [https://technotim.live/posts/homepage-dashboard/ Meet Homepage - Your HomeLab Services Dashboard]. Examples of yaml files in the config folder.
* [https://ettoreciarcia.com/publication/25-homepage/ Homepage: a single pain of glass for your Homelab]
<li>How-to:
<syntaxhighlight lang='sh'>
nano compose.yml # copy from https://github.com/gethomepage/homepage
                 # remember to the URLs on HOMEPAGE_ALLOWED_HOSTS 
mkdir config     # it's ok the folder is empty
docker compose up -d
nano config/services.yaml  # modify for our need
nano config/bookmarks.yaml # modify for our need
</syntaxhighlight>

<li>Tip: 
* By default, port 3000 is used.
* If I want to use port 80, make sure DO NOT INCLUDE ":80" to '''HOMEPAGE_ALLOWED_HOSTS''' in the compose.yml since browsers usually send the request with the Host header as just "homepage.local" (without ":80"). 
* To include [https://gethomepage.dev/widgets/services/pihole/ pihole] as a widget in the dashboard, I need to modify services.yaml. I also need to get the pihole api from Settings -> api. The api key is needed in order to access pihole statistics.

<li>Files under the config folder
<pre>
$ ls -t config/*.*
settings.yaml  widgets.yaml  bookmarks.yaml  services.yaml  docker.yaml  kubernetes.yaml  custom.css  custom.js
</pre>
It seems the most important ones are [https://gethomepage.dev/configs/services/ services.yaml] and [https://gethomepage.dev/configs/bookmarks/ bookmarks.yml]. Homepage automatically creates default/skeleton config files on first run inside /app/config if they do not already exist.

<li>[https://gethomepage.dev/configs/services/#icons Icons] 
* Icons can be specified by names. They are obtained from https://dashboardicons.com/.
* Local icons can be placed in a new folder 'icons' and use '''-v ./icons:/app/public/icons''' in docker command. Recall Homepage's web root is '''/app/public'''.
* Icons can be specified by using the way "/icons/myicon.png" in '''config/services.yaml''' file.
* Icons can be specified by full URLs.
* To download some website's favicon file, go to the source of a website and search for "icon". Alternatively, use a [https://onlineminitools.com/website-favicon-downloader web tool].
* Supported formats: .ico, .png, .svg, .webp
* Use '''docker compose restart homepage''' to see its effects.
<li>To hide the CPU usage, RAM, storage, and the search box in your Homepage dashboard, modify '''config/widgets.yaml''' file. If you want to hide the entire "resources" section, you can simply remove or comment out the entire - resources: block from your widgets.yaml.
<li>(Related to hide CPU/RAM/Storage/Search) To hide a horizontal bar at top (related to the header section), modify '''config/settings.yaml''' file by adding a line: '''headerStyle: none'''
<li>Examples :
* [https://github.com/epoch-philosophy/homepage-example epoch-philosophy]
</ul>

== Flame ==
https://github.com/pawelmalak/flame

== Homer ==
* https://github.com/bastienwirtz/homer
* [https://youtu.be/7re4LlJGBXE Homer Dashboard - Open Source, Self Hosted, Beautiful Shortcuts to all your sites and services], [https://youtu.be/9iTPm45EmxM This Homelab Dashboard is simple and beautiful!] (videos)

== Uptime Kuma ==
<ul>
<li>[https://hub.docker.com/r/louislam/uptime-kuma Docker], [https://github.com/louislam/uptime-kuma Github]
<li>[https://linuxiac.com/uptime-kuma-monitoring-tool-setup-guide/ Uptime Kuma Docker Setup Guide: Installation and Configuration]
<li>[https://youtu.be/tqgqFbxd7rg Uptime Kuma | Fancy service and server monitoring] (Video)
<li>Since I like to use Uptime Kuma to monitor servers using IPs from my tailscale, I need to expose host's network to the container. That is, I would use something like "docker run -d --network host louislam/uptime-kuma" or
<pre>
services:
  uptime-kuma:
    image: louislam/uptime-kuma:1
    container_name: kuma
    volumes:
      - ./data:/app/data
    network_mode: "host"  # Use host network mode
    restart: always
</pre>
Note 
* In host network mode, the container shares the network stack of the host directly, bypassing Docker's network isolation.
* The container can access all host network interfaces directly.
* Any ports exposed by the container are automatically accessible on the host without explicit port mapping.
* Port mapping is not applicable when the container is using host network. In host network mode, the container shares the network stack of the host system directly, bypassing Docker's network isolation.
</ul>

== heimdall ==
https://github.com/linuxserver/docker-heimdall

= Dashboard for monitoring system: grafana =
* [https://youtu.be/83LWo7h_hvs Docker Dashboard Using Grafana, Prometheus & Node Exporter] 
** [https://dbt3ch.com/books/prometheus-grafana-dashboard notes]
** My [https://gist.github.com/arraytools/c953e04c3e876681c1e7f8579bdcac83 own copy] of the two files '''prometheus.yml''' and '''docker-compose.yml '''
** Use '''docker-compose up -d''' or '''docker compose up -d''' to start the service.
* Another good tutorial: [https://youtu.be/9TJx7QTrTyo Server Monitoring // Prometheus and Grafana Tutorial] 2021
* When I try to create a new stack in Portainer, the error message is not clear.
* When I try it on a LXC container in Proxmox, I got an error '''ERROR: for node-exporter Cannot start service node-exporter: path / is mounted on / but it is not a shared or slave mount'''. This is the same error as some users reported. 
* It works when I try a regular container in Proxmox!
* [https://github.com/prometheus/node_exporter Node exporter]. The docker run command works if I run it in a regular Ubuntu system. You can check it is working by going to IP:9100.
** https://prometheus.io/docs/guides/node-exporter/
** curl http://localhost:9100/metrics works but using IP does not. So it is a firewall problem.
** [https://betterstack.com/community/guides/monitoring/monitor-linux-prometheus-node-exporter/ How to Monitor Linux Servers with Prometheus and Node Exporter]. '''sudo ufw allow 9090/tcp''' & '''sudo ufw allow 9100/tcp''' &  '''sudo ufw reload'''
* Use IP:9100 to check if Node Exporter works. Use IP:9090 to check if Prometheus works (Status -> Targets). Use '''IP:3457''' to access the Grafana where 3457 is the one I used in the docker-compose.yml ('''the default one is 3000''').
* Use admin/admin to log in. Add data source. Select Prometheus. Add the IP address, e.g., http://IP:9090.
* Google: node exporter grafana dashboards. https://grafana.com/grafana/dashboards/. E.g. [https://grafana.com/grafana/dashboards/11074-node-exporter-for-prometheus-dashboard-en-v20201010/ 11074] (1 Node Exporter for Prometheus Dashboard).

After I change the firewall by adding two ports (9090 & 9100), the docker-compose method of grafana works like a charm.

* Reboot the host OS will not affect the grafana (assuming we include '''restart: unless-stopped''' in the 3 containers). But if we modify docker-compose.yml and run ''docker-compose down; docker-compose up'' it will result in data lose and we will need to re-create the admin password and all the setup.

= Google keep =
== Joplin ==
* https://hub.docker.com/r/joplin/server
* [https://www.howtogeek.com/i-ditched-google-keep-for-this-self-hosted-note-taking-app/ I Ditched Google Keep for This Self-Hosted Note-Taking App]

= Google photo =
* [https://empty.coffee/photo-backup-bakeoff-photoprism-vs-immich-review/ Photo Backup Bakeoff: PhotoPrism vs Immich]

== Immich ==
* [https://github.com/immich-app/immich immich] - High performance self-hosted photo and video backup solution
* [https://immich.app/docs/overview/quick-start/ Quick Start]
* [https://www.makeuseof.com/raspberry-pi-immich-google-photos-alternative/ Immich Is a Great Google Photos Alternative You Can Host on Raspberry Pi]
* [https://missilepuppy.com/blog/2024/01/09/immich-finally-a-good-self-hosted-google-photos-replacement/ Immich – Finally, A Good Self-Hosted Google Photos Replacement]
* [https://linuxiac.com/how-to-install-immich-with-docker/ 9How to Install Immich with Docker: A Comprehensive Guide]
* [https://pimylifeup.com/immich-docker/ Setting up Immich using Docker[

== PhotoPrism ==
* [https://docs.photoprism.app/getting-started/docker/ PhotoPrism]

= ownCloud =
* https://hub.docker.com/_/owncloud/
* https://doc.owncloud.com/server/10.0/admin_manual/installation/docker/
* https://blog.securem.eu/serverside/2015/08/25/setting-up-owncloud-server-in-a-docker-container/
* [https://stackoverflow.com/questions/35137944/how-to-put-owncloud-behind-nginx-with-docker How to put ownCloud behind Nginx with Docker?]
* [https://www.blaize.net/2017/02/migrating-owncloud-to-docker/ Migrating ownCloud to Docker]
* "You are accessing the server from an untrusted domain" message when I use IP to access the server
** trusted_domains (config.php)
** https://forum.owncloud.org/viewtopic.php?t=34158 
** https://blog.securem.eu/serverside/2015/08/25/setting-up-owncloud-server-in-a-docker-container/
** [https://youtu.be/KUZu5XG6cjI Fix ownCloud accessing the server from an untrusted domain]
** '''My simple fix''': use the IP instead of localhost when opening the browser to set up the first time

After I use '''docker run --rm --name myowncloud -p 81:80 owncloud:8.1''', I find I can only access it through http://localhost:81. If I try to access it through another computer by http://xxx.xxx.xx.1:81, the URL is changed back to http://localhost:81 so it failed to load.

= nextcloud =
* https://hub.docker.com/_/nextcloud/
* https://github.com/nextcloud/docker
* [https://apps.nextcloud.com/ App store]
* [https://doc.owncloud.org/server/8.1/admin_manual/installation/apps_management_installation.html Installing and Managing Apps]
* Based on [https://github.com/owncloud owncloud's github repositories] or [https://github.com/nextcloud nextcloud's github repositories], android app has been updated more often than ios app.
* [https://youtu.be/Wj0SsbRbCNo Setting Up NextCloud on Docker w/ NGINX and CloudFlare for Remote Access!] (video)
* [https://www.wundertech.net/install-nextcloud-on-proxmox/ How to Install Nextcloud on Proxmox]
* [https://www.howtogeek.com/how-i-self-host-a-synced-password-manager/ How I Self-Host a Synced Password Manager]

Nextcloud looks more modern than owncloud though their interface are very similar. I got the same problem (URL is changed from IP to localhost) when I try to access its web from another computer. '''Using the IP instead of localhost to finish the initial setup can fix the error'''.

Note:
* The first we open the webpage, we need to create the admin username/password.
* Nextcloud uses owncloud mobile application.
* Nextcloud includes a small mp4 file. I can use browser to play mp4. Photos files can be opened in browsers too (including slideshow).

== Add external storage like SAMBA ==
To connect to a Samba drive in Nextcloud, you will need to use the '''External Storage''' app. This app allows you to mount external storage services, including Samba shares, as directories within your Nextcloud instance. Here are the steps to connect to a Samba drive in Nextcloud:

First, make sure that the '''External Storage''' app is installed and enabled on your Nextcloud instance. You can do this by going to the '''Apps''' section in the Nextcloud '''admin panel''' and searching for the External Storage app. If it is not installed, you can install it from there.

Once the External Storage app is installed and enabled, go to the Settings section in the Nextcloud admin panel and select the External Storages option under the '''Administration''' section (Left panel, scroll down to see the app).

On the External Storages page, click on the '''Add storage''' button and select SMB / CIFS from the dropdown menu.

In the configuration form that appears, enter the details of your Samba share, including the hostname or IP address of the server, share name, username, and password. You can also specify a subfolder within the share if you only want to mount a specific subfolder.

Once you have entered all of the required information, click on the Save button to save your configuration.

== [https://apps.nextcloud.com/ Nextcloud Apps] ==
* [https://docs.nextcloud.com/server/15/admin_manual/installation/installation_wizard.html#trusted-domains "access through untrusted domain" error]. On my Casaos, I found the file ''/DATA/AppData/nextcloud/var/www/html/config/config.php'' shows trusted domain is casaos.local:10081. So I just need to change the app's setting in CasaOS to use http://casaos.local:10081 instead of http://IP:10081 to open the page.
* [https://apps.nextcloud.com/apps/audioplayer Audio Player]. When I play mp3 files, the web interface does not show a progress bar:( <syntaxhighlight lang='bash'>
$ docker run --rm --name mynextcloud -v ~/Downloads/nextcloudapps:/var/www/html/custom_apps -p 81:80 nextcloud
# above will create an empty folder ~/Downloads/nextcloudapps (www-data:root)
$ tar xzvf Downloads/audioplayer-2.3.1.tar.gz -C Downloads/
$ docker cp Downloads/audioplayer mynextcloud:/var/www/html/custom_apps
# Go to nextcloud and '+Apps', a new app 'Audio Player' should have shown up.
</syntaxhighlight>
* [https://apps.nextcloud.com/apps/music Music]. GOOD. The app is from the owncloud team though for some reason the app is not included in owncloud/nextcloud. Yes, a progress bar is shown when I played a song downloaded from Youtube:) <syntaxhighlight lang='bash'>
# No need to create a volume
$ docker run -d --name mycloud -p 81:80 nextcloud

# Open another terminal
# Don't download the zip file from github. Get the zip file from the app store
$ tar xzvf ~/Downloads/music_0.7.0_nc-signed.tar.gz -C ~/Downloads/
$ docker cp Downloads/music mycloud:/var/www/html/custom_apps
$ docker exec mycloud chmod -R 0750 /var/www/html/custom_apps
$ docker exec mycloud chown -R www-data:www-data /var/www/html/custom_apps
</syntaxhighlight> Now open the website. Click the gear icon (Settings) and click "Apps". Find out the 'music' app from the bottom of the list and click the 'Enable' button. A new Music icon will be created next to the Gallery icon at the top. Note: if we want to play music repeatedly, I should not play the music directly from Files. I should click the Music icon at the top and let it start to scan musics. Then once I can play a music from there, it will show two new icons; one is shuffle and the other is loop. To have a persistent data, we can 'run' using <syntaxhighlight lang='bash'>
$ mkdir -p ~/nextcloud/{html,apps,config,data}
$ docker run -d \
    --name mycloud \
    -p 81:80 \
    -v ~/nextcloud/html:/var/www/html \
    -v ~/nextcloud/apps:/var/www/html/custom_apps \
    -v ~/nextcloud/config:/var/www/html/config \
    -v ~/nextcloud/data:/var/www/html/data \
    nextcloud
</syntaxhighlight> If we like to delete the contain and its unamed volume, run <syntaxhighlight lang='bash'>
$ docker stop mycloud; docker rm -v mycloud
</syntaxhighlight> If we run the container again mounting all volumes, all apps,files,configuration,admin's username & password are kept.
* '''PDF viewer'''. PDF files will be downloaded instead of opening on the browser. This can be easily fixed. Click '+Apps' from the personal settings (the response is slow when I tested using Docker). Search for '''PDF viewer'''. Click the 'Enable' button (it will be changed to 'Disable' after that)
* [https://apps.nextcloud.com/apps/drawio draw.io]. After enable it, we can click the "+" sign and choose "Diagram" to create a new diagram (*.xml).
* [https://apps.nextcloud.com/apps/radio Radio]. After enable it, a new "Radio" icon will be shown at the top. Only 20 stations are available from the 'Top'. No response after I clicked "Categories".

= Document management =
* [https://docs.paperless-ngx.com/ Paperless-ngx]
* [https://github.com/papra-hq/papra Papra], [https://www.youtube.com/watch?v=r3DdVXZ06Ho Video]

= Music: Navidrome =
[https://www.makeuseof.com/raspberry-pi-navidrome-self-hosted-music-server/ Navidrome Is the Perfect Self-Hosted Music Server for Raspberry Pi]

= FileRun =
* https://www.filerun.com/download
* [https://www.howtoforge.com/how-to-install-filerun-using-docker/ How to Install FileRun using Docker]
* [https://computingforgeeks.com/running-filerun-storage-sync-server-in-docker-container/ Running Filerun Storage Sync Server in Docker Container]. You can access, create and edit your files using Filerun via the web interface or the desktop sync app like NextCloud.
* [https://www.reddit.com/r/selfhosted/comments/8fbpjx/filerun_vs_nextcloud/ Filerun vs NextCloud?]

= File manager =

== File browser ==
* https://filebrowser.org/installation/, 
** https://github.com/filebrowser/filebrowser
** Default credential: admin/admin
* [https://youtu.be/30MYRgCObu8 Pi-Hosted : Installing JDownloader and File Browser On The Pi Docker Server Part 4] (video)
* It appears Filebrowser can only browse files in one directory from the same computer only. However, Filebrowser is not limited to browsing files in just one directory or from one computer only. While it is designed to operate from a specified "root" directory on the server where it is installed, it offers flexibility in how you configure access to multiple folders.
** '''Multiple Directories''': You can configure Filebrowser to access multiple directories by mapping several folders or disks as subdirectories within the main root directory you specify in your Docker (or other) setup. 
** '''Remote Folders''': If you want to access files on other computers, you need to mount those remote folders (such as Samba shares) onto the local filesystem of the server running Filebrowser.
** '''Multiple Servers''': If you want to manage files on multiple servers, you need to run an instance of Filebrowser on each server. There is no built-in feature to aggregate multiple servers into a single Filebrowser interface, but you can access each server’s Filebrowser web interface individually.

The original image (filebrowser/filebrowser) does not work but linuxserver's image (filebrowser/filebrowser:s6) works fine.
<syntaxhighlight lang='sh'>
$ touch filebrowser.db
$ cat settings.json
{
  "port": 80,
  "baseURL": "",
  "address": "",
  "log": "stdout",
  "database": "/database/filebrowser.db",
  "root": "/srv"
}

#  Modify $FULL_PATH1 <- directory to share files
#      &  $FULL_PATH2  <- directory contains filebrowser.db & settings.json

$ docker run \
    --name filebrowser \
    -v $FULL_PATH1:/srv \
    -v $FULL_PATH2/filebrowser.db:/database/filebrowser.db \
    -v $FULL_PATH2/settings.json:/config/settings.json \
    -e PUID=$(id -u) \
    -e PGID=$(id -g) \
    -p 8080:80 \
    filebrowser/filebrowser:s6
</syntaxhighlight>

== Quantum ==
https://github.com/gtsteffaniak/filebrowser. It supports multiple sources!

== FilGator ==
https://filegator.io/

= Seafile =
* https://en.wikipedia.org/wiki/Seafile. Seafile's functionality is similar to other popular file hosting services such as Dropbox and Google Drive.
* [https://itsfoss.com/deploy-seafile-server-docker/ How to Deploy Seafile Server with Docker to Host Your Own File Synchronization and Sharing Solution]

= Run a Linux desktop =

== Run a Linux desktop VM with VNC ==
[https://computingforgeeks.com/run-ubuntu-linux-in-docker-with-desktop-environment-and-vnc/ Run Ubuntu Linux in Docker with Desktop Environment and VNC]

== Webtop ==
* See [[#Webtop:_Linux_desktop_in_a_browser|Guacamole - Webtop]]
* Each Docker run will create one linux desktop

== Kasm Workspaces ==
* https://www.kasmweb.com/community-edition
** [https://www.kasmweb.com/docs/latest/install/single_server_install.html Installation Guide]
** Kasm UI Login Credentials & Database Credentials are listed after the installation is complete. It's good to save the information.
* Kasm Workspaces includes several Linux Desktop already. 
* [[Docker#Linux_in_browser|Linux in browser]]

== Distrobox & BoxBuddy (No Desktop) ==
<ul>
<li>https://github.com/89luca89/distrobox (in the 'Installation' section there is a table. It seems the green color is used to show which Linux distributions has the latest version of distrobox)
* Idea: Distrobox uses containerization technologies like '''Podman, Docker''', or '''LXC''' to create '''containers''' with your chosen Linux distribution (Why worry about Podman/LXC?)
* Important: Since it integrated with the host system, '''always back up important data and double-check configurations to avoid unintended changes. Changes may happen when we use a software (eg install R packages) launched from a box.'''
* Practical uses:
** Running GUI Applications from Other Distros (Containers): distrobox-enter fedora-box -- firefox
*** (not tested) OnlyOffice (Ubuntu/Debian, CentOS/RHEL, snap, flatpak, appimage). 1. Install Distrobox on Manjaro '''sudo pacman -Syu && sudo pacman -S distrobox''', 2. Create an Ubuntu container '''distrobox create --image ubuntu:latest --name ubuntu-container''' , 3. Enter the Ubuntu container '''distrobox enter ubuntu-container''', 4. Update package lists and install ONLYOFFICE Desktop Editor '''sudo apt install onlyoffice-desktopeditors''', 5, Run ONLYOFFICE Desktop Editors '''onlyoffice-desktopeditors'''.
** Developing and Testing on Multiple Linux Distributions
** Using Up-to-Date Tools on Older Systems
** Lightweight Alternative to Virtual Machines
** Persistent Workflows Across Systems: the created container is tightly integrated with the host, allowing sharing of the HOME directory (yes, no extra configuration), external storage, USB devices
** Running Different Package Managers: Use Arch's pacman or Fedora’s dnf on a system where apt is the native package manager. 

<li>[https://www.howtogeek.com/how-to-install-and-use-distrobox/ How I Break Linux's Rules and Install Any Package on Any Distro]
<li>[https://wiki.archlinux.org/title/Distrobox Archwiki]

<li>Installation
* Distribution's version 
* PPA for Ubuntu https://launchpad.net/~michel-slm/+archive/ubuntu/distrobox
* Installation script provided by distrobox. "curl -s https://raw.githubusercontent.com/89luca89/distrobox/main/install | sudo sh". See [https://idroot.us/install-distrobox-debian-12/ How To Install Distrobox on Debian 12]

<li>[https://www.howtogeek.com/run-any-app-on-any-linux-distro-with-distrobox/ DEB Files on Arch? Run Any App on Any Linux Distro With This Tool]

<li>[https://itsfoss.com/distrobox/#4-integration-of-distrobox-applications Distrobox: Try Multiple Linux Distributions via the Terminal]. The line "distrobox-export --app foliate" gives an error "cannot find any desktop files".
<li> [https://youtu.be/Sj064D9ZUl8 Stop Distro Hopping! Use this AWESOME tool on Linux] 7/15/2023
* Linux subsystem in another Linux
<li>[https://www.maketecheasier.com/run-program-from-any-linux-distro-with-distrobox/ How to Run Any Program from Any Linux Distro with Distrobox]
<li>Testing using arch linux container where packages are always updated. Refer to [https://github.com/89luca89/distrobox/blob/main/docs/usage/distrobox-create.md distrobox create] doc for examples.
{{Pre}}
sudo apt install distrobox
distrobox --version # 1.7.0

distrobox create # default is fedora-toolbox:XX

distrobox-create --name ubuntu2404 -i ubuntu:24.04 # same as docker.io/library/ubuntu:24.04

distrobox-create --name arch --pull -i quay.io/toolbx/arch-toolbox:latest
distrobox enter arch # slow on Celeron N3160 Udoo

cat /etc/os-release  # guest
uname -r             # still host
sudo pacman -Syu     # update the entire arch linux system
sudo pacman -S r     # install R
R                    # plotting also works
sudo pacman -S netsurf
sudo pacman -R netsurv
sudo pacman -S vivaldi
sudo pacman -Sy chromium 
# Arch Linux Package Search:
# https://archlinux.org/packages/?q=browser&sort=-last_update
# and sort by 'Last Updated'
chromium &            # so prompt is returned 

distrobox-list

podman images # list image's size; podman is the default container manager on my debian
              # possibly 'docker images'

distrobox-rm ubuntu2404
</pre>
Use GUI Applications from the Container
<pre>
apt install x11-apps -y
xeyes
</pre>
<li>'''add-apt-repository command not found''' in Ubuntu box. This happened when I try to run a command like "sudo add-apt-repository ppa:rvm/smplayer".
<pre>
sudo apt update
sudo apt install soft-properties-common
</pre>
<li>List of compatible images and container managers, [https://github.com/89luca89/distrobox/blob/main/docs/compatibility.md#containers-distros Compatibility] page.
<li>Some images works fine on my distrobox 1.7.0
* quay.io/toolbx/arch-toolbox:latest
* docker.io/library/archlinux:latest
* registry.fedoraproject.org/fedora-toolbox:35
* docker.io/library/debian:bullseye-backports
* quay.io/toolbx-images/debian-toolbox:12

<li>Change the default container manager. distrobox-create --help.
<pre>
DBX_CONTAINER_MANAGER="docker"
</pre>

<li>distrobox-export --app XXX
* This is to export an application to the host system
* It seems there is no way to undo it. We need to enter the guest OS, remove the app and then remove the guest OS from the host.

</ul>

=== Atoms ===
* Easily manage Linux Chroot(s) and Containers with Atoms. https://github.com/AtomsDevs/Atoms (421 stars)
* [https://www.linuxlinks.com/useful-free-open-source-distrobox-gui-tools/ 4 Useful Free and Open Source Distrobox GUI Tools]

=== BoxBuddy ===
* https://www.dvlv.co.uk/BoxBuddyRS/ & https://github.com/Dvlv/BoxBuddyRS. Currently it is 2.5.5 (443 stars)
* [https://www.linuxlinks.com/boxbuddy-graphical-manager-distrobox/ BoxBuddy – graphical manager for Distrobox]
* The advantage is it includes a list of all distributions. Users only need to select one and enter a name for the 'box'.
* Install by '''flatpak install flathub io.github.dvlv.boxbuddyrs''' (no need to download flatpakref file)
* How does the software keep an updated list of images?
* Tested: 
** install Debian12, 
** install sublime deb inside Debian12 through host's right click button. Sublime can be launched too from "View Applications".
** Upgrade my arch Box (rolling release) works

== QuickEmu (Non Docker approach) ==
See [[KVM#QuickEMU|KVM - QuickEmu]]/

= Guacamole =
* Guacamole is nothing more than a centralized front end to access multiple VNC/RDP devices. You are still using either VNC or RDP to access the device.
* Probably there is no point to use Guacamole if the VM was created in Proxmox since Proxmox provides a web interface to access the VM.
* [https://youtu.be/DGw6P5Lkj-U Guacamole Remote Desktop - Open Source, Self Hosted remote access to your machines in the browser!] (video). https://github.com/jwetzell/docker-guacamole
** One line script to install Docker-CE, Docker-Compose, Portainer-CE (not needed), and NGinX Proxy manager (not needed)
** Once creating docker-compose.yml, we can fire up it using '''docker-compose up -d'''
** We can create a new admin user and delete the default username/password guacadmin/guacadmin
** Open a browser tab and go to the IP:Port to open guacamole web page
** We can add various connections (Kubenetes/RDP/SSH/Telnet/VNC). After that, we can run connections through our web browser.
** After saving the new connection, go back to "Home" to use the new connections.
* [https://youtu.be/Mjrj6tdj1wo Guacamole Remote Access Gateway on Docker] (video). https://github.com/boschkundendienst/guacamole-docker-compose works fine. Your guacamole server should now be available at '''https'''://ip:8443/. The default username is '''guacadmin''' with password '''guacadmin'''. Four containers will be launched: nginx, postgres, guacamole and guacd.
* [https://youtu.be/tg1CbMEzCsc How To Access Your PCs and Servers from Anywhere Using Guacamole and CloudFlare Tunnels]

== Webtop: Linux desktop in a browser ==
* https://hub.docker.com/r/linuxserver/webtop/, or https://github.com/linuxserver/docker-webtop. Ubuntu, Alpine, Arch, and Fedora based Webtop images, Linux in a web browser supporting popular desktop environments.
* An example. It seems the host's Disk space, Memory are all passed to VM. In this example, the host's directory "/tmp/downloads" will serve as the HOME directory in VM.
:<syntaxhighlight lang='sh'>
mkdir /tmp/downloads/
docker run -d --name=webtop   \
  -e PUID=1000 -e PGID=1000   \
  -e TZ=US/Eastern   \
  -p 3000:3000   \
  -v /tmp/downloads:/config   \
  --shm-size="1gb"   \
  --restart unless-stopped   \
  linuxserver/webtop:ubuntu-xfce
</syntaxhighlight>
* [https://www.linuxserver.io/blog/2021-05-05-meet-webtops-a-linux-desktop-environment-in-your-browser Meet Webtops A Linux Desktop Environment In Your Browser]
* [https://youtu.be/bQrtnZ1UrQQ Run Linux Desktops in your Browser with Docker and Webtops!] (video) and [https://wiki.opensourceisawesome.com/books/webtops-for-remote-sessions/page/webtops-linux-desktops-in-docker Notes]
* Default username/password is abc/abc. But we don't need to enter the password when we use "sudo".
* [https://youtu.be/Gd9bvdkIXOQ Linux desktop, inside of a container, inside of a browser??? Yes. A Webtop], [https://youtu.be/Gd9bvdkIXOQ?t=811 privileged: true] is required for installing something like vscode in VM (video) and [https://docs.technotim.live/posts/webtop-container/ Doc]
* If I'm not using the default desktop, I need to switch to use some user's account instead of root to run docker-compose command. If I use root to launch ubuntu-kde, for example, the desktop is blank.
* It's cool. I got Ubuntu 22.04 released 1.5 months ago.
* After I installed 'htop', the htop command shows the cpu & memory & uptime ... from the 'host' system. But  '''docker stats''' shows webtop (ubuntu-mate) desktop is using around 300MB memory.
* When I want to copy text from VM to remote client, I need to open the clipboard using the black circle tool on the left-hand side. 
* After I played around, KDE-konsole does not respond to my keyboard. Logged out and logged in again fixes the problem.
* I got the following errors when I try to install RStudio 2022.02.3 Build 492 on Ubuntu 22.04; this solution [https://stackoverflow.com/a/71969930 Installing R Studio on Ubuntu 22.04] works for me.
<div style="margin-left: 2em;">
<pre>
$ sudo apt install /config/Downloads/rstudio-2022.02.3-492-amd64.deb 
the following packages have unmet dependencies:
 rstudio : Depends: libssl1.0.0 but it is not installable or
                    libssl1.0.2 but it is not installable or
                    libssl1.1 but it is not installable
</pre>
</div>
* Since the ''config'' subfolder is mounted, if we want to try different flavors of Linux/Desktop, we should create different folders.
* From scratch [https://youtu.be/8IfTXJRAIJw From Start to Finish Build a Desktop on a Browser Docker Container]

== instantbox ==
* [https://github.com/instantbox/instantbox instantbox]
* [https://www.makeuseof.com/instantbox-access-linux-distro-in-web-browser/ Instantbox Gives You Instant Access to a Linux Distro in a Web Browser]

= IDE =

== cloud9 ==
https://hub.docker.com/r/linuxserver/cloud9

== VS Code ==
* [https://github.com/coder/code-server code-server] VS Code in the browser. https://hub.docker.com/r/codercom/code-server
* [https://www.reddit.com/r/docker/comments/waebx5/development_container_with_visual_studio_code_how/ Development container with Visual Studio code - how does it work?]
* [https://coder.com/docs/v2/latest/quickstart/docker Coder] - Your Self-Hosted Remote Development Platform
** Instruction step 1 is necessary
** Workspace - Template
** After issuing docker run command, I need to go to the URL, create username/password. The username is for the app login purpose. 
** Add & Start the Template.
** For the VS-code template, I can launch a Terminal and work on it (Same RAM as my machine, 6GB storage of Debian image).
* [https://hub.docker.com/r/gitpod/openvscode-server OpenVSCode Server] 1M+ pulls. [https://github.com/coder/code-server/discussions/4267 Difference to OpenVSCode Server].

= Docker for R (r-base, rstudio) =
See [[R_Docker|R Docker]].

= Docker for Shiny Server =
<ul>
<li>[https://hosting.analythium.io/user-2022-best-practicesfor-shiny-apps-with-docker-and-more/ UseR!2022: Best Practices for Shiny Apps with Docker and More]
<li>[https://hosting.analythium.io/containerizing-interactive-r-markdown-documents/ Containerizing Interactive R Markdown Documents] 2022/7
<li>By default, Shiny Server looks for either:
* A single-file Shiny app named '''app.R''' in the root of a directory.
* A pair of files named '''ui.R''' and '''server.R''' within a directory.
<li>[https://datawookie.dev/blog/2022/09/using-shiny-server-in-docker/ Using Shiny Server in Docker] 2022/9/7. Hello world example. Need to generate ''Dockerfile''.
<pre>
FROM rocker/shiny:4.1.0
RUN rm -rf /srv/shiny-server/*
WORKDIR /srv/shiny-server/
COPY ./app.R ./app.R
</pre>
<pre>
docker build -t shiny-in-docker .
docker run --rm -p 3838:3838 shiny-in-docker
</pre>
<li>https://hub.docker.com/r/rocker/shiny/. Pay attention to the [https://hub.docker.com/r/rocker/shiny/~/dockerfile/ Dockerfile] there.
{{Pre}}
# sudo mkdir /srv/
sudo mkdir /srv/shinylog
sudo mkdir /srv/shinyapps
cd /srv/shinyapps
sudo wget https://raw.githubusercontent.com/rstudio/shiny-examples/master/050-kmeans-example/ui.R
sudo wget https://raw.githubusercontent.com/rstudio/shiny-examples/master/050-kmeans-example/server.R
sudo lsof -i -P -n | grep LISTEN    # nmap localhost
docker run -d --restart always -p 3838:3838  \
   -v /srv/shinyapps/:/srv/shiny-server/  \
   -v /srv/shinylog/:/var/log/shiny-server/  \
   rocker/shiny:4.0.3
nmap localhost
</pre>
If the 3838 port method (http://IP:3838) works, we can move on to use Nginx + reverse proxy method; see [[Apache#R.2FShiny_example|Apache->R/Shiny example]] for the instruction.
</li>
</ul>
* [http://docs.rstudio.com/shiny-server/ Shiny Administrator Guide]
* [https://docs.docker.com/engine/reference/commandline/run Docker Reference]. See Engine (docker) CLI from their LHS.
* [http://www.flaviobarros.net/2015/04/30/dockerizing-a-shiny-app/ Dockering a shiny app]
* [https://hosting.analythium.io/dockerizing-shiny-applications/ Dockerizing Shiny Applications]
<ul>
<li>[https://biolitika.si/pin-r-package-versions-using-docker-and-renv.html Pin package versions in your production Docker image]. Need to modify Dockerfile to install 'shiny' along with 'renv'. We need to create a directory 'shinyapp' with simple shiny files (eg [https://shiny.rstudio.com/gallery/kmeans-example.html kmeans] example).
{{Pre}}
docker build -t pinrpackageversion .
mkdir shinyapp
wget https://raw.githubusercontent.com/rstudio/shiny-examples/master/050-kmeans-example/ui.R -P shinyapp
wget https://raw.githubusercontent.com/rstudio/shiny-examples/master/050-kmeans-example/server.R -P shinyapp
docker run --name shinyapp --rm -p 3838:3838 pinrpackageversion
</pre>
</li>
<li>Question: what happened if there is a new version of R or shiny-sever?
<syntaxhighlight lang='bash'>
# specify --name so we don't need to use container id to access it later
$ docker run -d --name rshiny -p 81:3838 rocker/shiny 

$ docker ps -l

# Run in container's bash
# https://stackoverflow.com/questions/30172605/how-to-get-into-a-docker-container
# non-interactive
$ docker exec -it rshiny ip addr  
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default qlen 1
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
    inet 127.0.0.1/8 scope host lo
       valid_lft forever preferred_lft forever
22: eth0@if23: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue state UP group default 
    link/ether 02:42:ac:11:00:02 brd ff:ff:ff:ff:ff:ff link-netnsid 0
    inet 172.17.0.2/16 scope global eth0
       valid_lft forever preferred_lft forever

# interactive shell
$ docker exec -it rshiny bash 
root@5b78988d5619:/# who
root@5b78988d5619:/# which R
/usr/bin/R
root@5b78988d5619:/# ls /home
docker	shiny
root@5b78988d5619:/# ls /srv/shiny-server
01_hello  02_text  03_reactivity  04_mpg  05_sliders  06_tabsets  07_widgets  08_html  09_upload  10_download  11_timer  index.html  sample-apps
root@5b78988d5619:/# R -e 'package.Description("glmnet")'
root@5b78988d5619:/# exit

$ docker stop rshiny
$ docker rm rshiny   # remove the container
</syntaxhighlight>
</li>
</ul>

It is also useful to use the '''-v''' option in '''docker run''' so the local directory (eg /srv/shinyapps/) can be mapped to the docker volume (/srv/shiny-server).
<syntaxhighlight lang='bash'>
# Put your shiny app in host's /srv/shinyapps/appdir,
$ docker run -d -p 81:3838 \
    -v /srv/shinyapps/:/srv/shiny-server/ \
    -v /srv/shinylog/:/var/log/shiny-server/ \
    rocker/shiny
</syntaxhighlight>
And check running status
<pre>
$ docker ps -a
</pre>

== R packages installation: packrat ==
* https://cran.r-project.org/web/packages/packrat/index.html
* [https://github.com/joelnitta/docker-packrat-example Installing R packages to a Docker image with packrat]
* [https://community.rstudio.com/t/how-to-install-packages-through-packarat-while-creating-shiny-docker-image/27677 How to install packages through `packrat` while creating shiny Docker image]

== Check opened ports ==
See [[Linux#What_network_ports_are_open:_lsof_or_netstat|What network ports are open: lsof or netstat]].
<pre>
$ netstat -ant
Active Internet connections (servers and established)
Proto Recv-Q Send-Q Local Address           Foreign Address         State      
tcp        0      0 0.0.0.0:22              0.0.0.0:*               LISTEN     
tcp        0      0 127.0.0.1:25            0.0.0.0:*               LISTEN     
...
tcp6       0      0 :::80                   :::*                    LISTEN     
tcp6       0      0 :::81                   :::*                    LISTEN     
tcp6       0      0 :::22                   :::*                    LISTEN     
tcp6       0      0 ::1:25                  :::*                    LISTEN
</pre>

== Blog Explorer ==
https://github.com/nz-stefan/blog-explorer, [https://blog.rstudio.com/2020/07/13/winners-of-the-2nd-shiny-contest/ Winners of the 2nd Annual Shiny Contest]

== Raspberry Pi ==
[https://www.brodrigues.co/blog/2020-09-20-shiny_raspberry/ The Raspberry Pi 4B as a shiny server]

= BioContainers =
* https://biocontainers.pro/#/
* https://hub.docker.com/u/biocontainers/
* https://github.com/BioContainers

= CMS, blog website =
== Ghost ==
* [https://www.howtoforge.com/tutorial/docker-guide-deploying-ghost-blog-with-mysql-and-traefik-with-docker/ Deploying Ghost Blog with MySQL and Traefik with Docker]
* [https://youtu.be/20PBLsWC8Ms Host a Ghost CMS Website in Docker] (video)

= Proxy =
* Best proxy - traefik, NPM, SWAG, caddy or other?
* [https://github.com/linuxserver/docker-swag swag]

== Nginx proxy manager ==
* [https://youtu.be/cjJVmAI1Do4 Putting it All Together - Docker, Docker-Compose, NGinx Proxy Manager, and Domain Routing - How To] (video) and [https://shownotes.opensourceisawesome.com/putting-it-all-together/ Notes] 2020-10-06
* [https://youtu.be/UfCkwlPIozw Securing NGinX Proxy Manager - follow up - securing your admin console for this Open Source Software] (video) and [https://shownotes.opensourceisawesome.com/securing-nginx-proxy-manager/ Notes] 2020-10-20

== Caddy ==
* [https://github.com/rocker-org/rocker/issues?q=caddy Rocker], [https://www.rocker-project.org/use/networking/ Networking: tips and tricks] from Rocker
* [https://youtu.be/tv4A39yDDXs?t=526 Pi-Hosted : Reverse Proxy with Caddy]. We can play Caddy using IP address.
* [https://linuxiac.com/how-to-set-up-caddy-as-reverse-proxy/ How to Set up Caddy as a Reverse Proxy]
* [https://www.youtube.com/watch?v=qj45uHP7Jmo Reverse Proxy And Auto SSL Using Caddy And Docker Compose] (short video). Combine portainer and caddy in one compose.yml file.

= Website analysis =
* [https://www.howtoforge.com/how-to-install-plausible-analytics-with-docker-on-ubuntu-22-04/ How to Install Plausible Analytics with Docker on Ubuntu 22.04]

= Nginx =
<ul>
<li>[https://www.nginx.com/blog/deploying-nginx-nginx-plus-docker/ Using the NGINX Open Source Docker Image]
<pre>
docker run -d --name web \
  -p 8080:80 \
  nginx
curl http://localhost:8080
docker exec -it NGINX_container_ID bash
</pre>
<li>Note nginx docker does not work if there is not index.html or index.php (it shows '''403 Forbidden'''). Google: '''How to serve static file with nginx'''
* [https://sabe.io/tutorials/serve-static-files-nginx-docker How to Serve Static Files with Nginx and Docker]
* [https://serverfault.com/a/738067 How To Serve Static File Directory Over HTTP Using NGINX]
* [https://fedingo.com/how-to-serve-static-files-from-different-folder-in-nginx/ How to Serve Static Files from Different Folder in NGINX]
<li>[https://www.docker.com/blog/how-to-use-the-official-nginx-docker-image/ How To Use the Official NGINX Docker Image]
<pre>
docker run -it --rm -d \
  -p 8080:80 \
  --name web \
  -v ~/Downloads/html:/usr/share/nginx/html \
  nginx

docker stop web # when finished
</pre>
<li>[https://www.cloudsavvyit.com/5167/how-to-run-nginx-inside-docker-for-easy-auto-scaling/ How to Run NGINX Inside Docker (for Easy Auto-Scaling)]
<li>[https://www.digitalocean.com/community/tutorials/how-to-run-nginx-in-a-docker-container-on-ubuntu-14-04 How To Run Nginx in a Docker Container on Ubuntu 14.04]. It teaches to put the whole web site in the host directory and the nginx configuration in the local host. You can edit the default file locally (to serve a new directory), or to use a '''proxy_pass''' to forward the traffic to another app/container like you would with a regular Nginx installation). 
<li>[https://www.digitalocean.com/community/tutorials/docker-explained-how-to-containerize-and-use-nginx-as-a-proxy How To Containerize and Use Nginx as a Proxy]
<li>[https://blog.docker.com/2015/04/tips-for-deploying-nginx-official-image-with-docker/ TIPS FOR DEPLOYING NGINX (OFFICIAL IMAGE) WITH DOCKER]
<li>[https://linux.cn/article-8932-1.html Docker 快速入门]
<li>[https://www.nginx.com/blog/deploying-nginx-nginx-plus-docker Deploying NGINX and NGINX Plus with Docker]
<li>[https://www.linux.com/learn/intro-to-linux/2017/11/how-install-and-use-docker-linux How to Install and Use Docker on Linux] Reverse-proxy, LetsEncrypt ... built in.
<syntaxhighlight lang='bash'>
docker run --name docker-nginx -p 80:80 nginx

docker run --name my-nginx \ 
    -v /host/path/nginx.conf:/etc/nginx/nginx.conf:ro \
    -v /some/html:/usr/share/nginx/html:ro \
    -p 8080:80 \
    -d nginx
</syntaxhighlight>
</ul>

= httpd/apache =
https://hub.docker.com/_/httpd/

<ul>
<li>[https://www.tecmint.com/install-apache-web-server-in-a-docker-container/ How to Setup a Simple Apache Web Server in a Docker Container]
<li>[https://codingbee.net/docker/docker-an-apache-hello-world-example Docker – An apache ‘hello world’ example]
<li>Note nginx docker does not work if there is not index.html or index.php (it shows '''403 Forbidden'''); httpd image does not have this problem.
<pre>
docker run -d --rm\
  --name apache \
  -p 8080:80 \
  -v /home/brb/Videos/:/usr/local/apache2/htdocs/ \
  httpd
</pre>
</ul>

= Tomcat =
https://hub.docker.com/_/tomcat/

= ASP.NET =
* [https://blog.pankajgarg.com/helloaspnetcoreonpi/ Running ASP.NET core web application on Raspberry Pi]
* [https://hub.docker.com/_/microsoft-dotnet-framework-aspnet ASP.NET] by Microsoft

= Forum =
[https://www.howtoforge.com/how-to-install-discourse-forum-with-docker-on-centos-8/ How to Install Discourse Forum with Docker on CentOS 8]

= Jenkins for continuous integration =
* https://www.tutorialspoint.com/jenkins/jenkins_overview.htm
* https://jenkins.io/doc/book/installing/
* Example: https://dev.ropensci.org/

= MySQL =
* https://hub.docker.com/r/mysql/mysql-server/
* [https://dev.mysql.com/doc/mysql-installation-excerpt/5.7/en/linux-installation-docker.html Deploying MySQL on Linux with Docker]
* Note it seems impossible to use the 'grant' command interactively within the MySQL docker container.
* https://dzone.com/articles/using-docker-to-create-a-mysql-server <syntaxhighlight lang='bash'>
docker run --detach --name test-mysql --env="MYSQL_ROOT_PASSWORD=mypassword" mysql
docker inspect test-mysql | grep IPAddress  # 172.17.0.2

# https://dev.mysql.com/doc/index-other.html
wget -O - http://downloads.mysql.com/docs/world.sql.gz | gunzip -c > world.sql

mysql -uroot -pmypassword -h 172.17.0.2 -e 'CREATE DATABASE world'
cat world.sql | mysql -uroot -pmypassword -h 172.17.0.2 world
# zcat world.sql.gz | mysql -uroot -pmypassword -h 172.17.0.2 world
mysql -uroot -pmypassword -h 172.17.0.2 -e 'USE world; SHOW TABLES'

mysql -uroot -pmypassword -h 172.17.0.2 -e 'DROP DATABASE world'
</syntaxhighlight>  <syntaxhighlight lang='rsplus'>
# Let's see if we can access the database in R
system("sudo apt install libmysqlclient-dev")
library(RMySQL)
con <- dbConnect(MySQL(), "world", user="root", password="mypassword", host="172.17.0.2")
dbListTables(con)
head(dbReadTable(con, "city"))
head(dbReadTable(con, "country"))
head(dbReadTable(con, "countrylanguage"))

dbWriteTable(con, 'iris', iris)
# Error in .local(conn, statement, ...) :
#   could not run statement: The used command is not allowed with this MySQL version
dbDisconnect(con)
</syntaxhighlight>
* [https://youtu.be/w_aVnMmrASE How To Create And Test MySQL Database Server in Docker On Ubuntu Linux] (video). Use Dockerfile.
* [https://severalnines.com/blog/mysql-docker-containers-understanding-basics MySQL Docker Containers: Understanding the basics], https://youtu.be/qJQPckRYNis?t=16m29s <syntaxhighlight lang='bash'>
# Fire up
docker run --detach --name=test-mysql --env="MYSQL_ROOT_PASSWORD=mypassword" mysql
docker ps -a

# Connecting to the Container
docker inspect test-mysql | grep IPAddress
# sudo apt install mysql-client
# There are two methods to connect to the container
# method 1. https://hub.docker.com/r/mysql/mysql-server/
# docker exec -it test-mysql mysql -uroot -p
# method 2
mysql -uroot -pmypassword -h 172.17.0.20 -P 3306
docker run --detach --name test-wordpress --link test-mysql:mysql wordpress
docker exec -it test-wordpress bash
$ cat /etc/hosts

# Expose the MySQL container to the outside world
# Access the MySQL container directly from the machine’s port 6603
docker run --detach --name=test-mysql --env="MYSQL_ROOT_PASSWORD=mypassword" --publish 6603:3306 mysql
mysql -u root -pmypassword -h 127.0.0.1 -P 6603

# Configuration management
mkdir -p /root/container/test-mysql/conf.d
nano /root/container/test-mysql/conf.d/my-custom.cnf
docker run \
    --detach \
    --name=test-mysql \
    --env="MYSQL_ROOT_PASSWORD=mypassword" \
    --publish 6603:3306 \
    --volume=/root/docker/test-mysql/conf.d:/etc/mysql/conf.d \
    mysql
mysql -uroot -pmypassword -h127.0.0.1 -P6603 -e 'show global variables like "max_connections"';
docker run \
    --detach \
    --name=test-mysql \
    --env="MYSQL_ROOT_PASSWORD=mypassword" \
    --publish 6603:3306 \
    mysql \
    --max-connections=200 \
    --character-set-server=utf8mb4 \
    --collation-server=utf8mb4_unicode_ci

# Data Storage
mkdir -p /storage/docker/mysql-datadir
docker run \
    --detach \
    --name=test-mysql \
    --env="MYSQL_ROOT_PASSWORD=mypassword" \
    --publish 6603:3306 \
    --volume=/root/docker/test-mysql/conf.d:/etc/mysql/conf.d \
    --volume=/storage/docker/mysql-datadir:/var/lib/mysql \
    mysql
docker inspect test-mysql
ls -al /storage/docker/mysql-datadir/

# If a MySQL container runs on top of an existing MySQL datadir, 
# the $MYSQL_ROOT_PASSWORD variable should be omitted from the “run” command line;
docker stop test-mysql
docker rm -f test-mysql
docker run -d --name=another-new-mysql -p 6605:3306 -v /storage/docker/mysql-datadir:/var/lib/mysql mysql
docker logs another-new-mysql
</syntaxhighlight>
* [https://codereviewvideos.com/course/docker-tutorial-for-beginners/video/docker-mysql-tutorial Use Docker to run a typical MySQL server] from Code Review Videos <syntaxhighlight lang='bash'>
docker volume create crv_mysql

docker run \
    -e MYSQL_ROOT_PASSWORD=my-secret-pw \
    -e MYSQL_DATABASE=devdb \
    -e MYSQL_USER=dbuser \
    -e MYSQL_PASSWORD=dbpassword \
    --mount type=volume,src=crv_mysql,dst=/var/lib/mysql \
    -p 3306:3306 \
    -d \
    mysql:latest

# Alternatively we can put username/password in a text file for security
cat > .env <<EOF
MYSQL_ROOT_PASSWORD=my-secret-pw
MYSQL_DATABASE=devdb
MYSQL_USER=dbuser
MYSQL_PASSWORD=dbpassword
EOF
docker run \
    --env-file .env \
    --mount type=volume,src=crv_mysql,dst=/var/lib/mysql \
    -p 3306:3306 \
    -d \
    mysql:latest
</syntaxhighlight>

== Backup and restore ==
* https://gist.github.com/spalladino/6d981f7b33f6e0afe6bb
* [[MySQL#How_to_backup.2Fexport_and_load.2Fimport_a_single_database_and.2For_table_from_a_MySQL_database|MySQL]] page
<syntaxhighlight lang='bash'>
# Backup
docker exec CONTAINER /usr/bin/mysqldump -u root --password=root DATABASE > backup.sql

# Restore
# Method 1. docker exec + command
docker exec -i CONTAINER /usr/bin/mysql -u root --password=root < backup.sql
# Method 2. docker exec + bash
# We can also use docker exec log into the contain and run any mysql commands there
docker exec -it CONTAINER bash
# Method 3. mysql command only
# We directly use mysql command to import database without using docker commands
#   as long as we know the IP address of the container server
docker inspect CONTAINER | grep IPAddress
mysql -uroot -pPASSWORD -h 172.18.0.3 -e 'show databases'
mysql -uroot -pPASSWORD -h 172.18.0.3 < backup.sql
</syntaxhighlight>

= PostgreSQL =
* [https://markheath.net/post/exploring-postgresql-with-docker Exploring PostgreSQL with Docker]
* [https://colinfay.me/clients-db/ clientsdb - A docker image with clients comments]. See [[MySQL#Docker_server_.2B_R_client|here]].

= Jekyll =
[https://martinpeck.com/blog/2020/11/05/building-jekyll-with-vscode-devcontainers/ Building Jekyll Sites within VS Code Dev Containers]

= node.js =
[https://medium.com/openmindonline/js-monday-13-dockerizing-node-js-e09d5f8bf945 Dockerizing Node.js]. See the code [https://github.com/arraytools/dockerizenode here].
<pre>

$ docker build -t my-node-app .
$ docker run -p 3000:3000 my-node-app
</pre>

[https://www.docker.com/blog/how-to-setup-your-local-node-js-development-environment-using-docker/ How To Setup Your Local Node.js Development Environment Using Docker] (not working)
{{Pre}}
$ cd notes-service
$ cat Dockerfile 
FROM node:12.18.1

WORKDIR /code

COPY package.json /code/package.json
COPY package-lock.json /code/package-lock.json

RUN npm install

COPY . /code

CMD [ "node", "server.js" ]

$ docker build -t notes-service .
$ docker run -it --rm -d -v mongodb:/data/db -v mongodb_config:/data/configdb -p 27017:27017 --network mongodb --name mongodb mongo
$ docker run -it --rm -d --network mongodb --name notes -p 8081:8081 -e SERVER_PORT=8081 -e DATABASE_CONNECTIONSTRING=mongodb://mongodb:27017/yoda_notes notes-service 
# this does not work though no errors; omit "-d" to see the error message

$ curl --request POST \
--url http://localhost:8081/services/m/notes \
  --header 'content-type: application/json' \
  --data '{
"name”: "this is a note",
"text": "this is a note that I wanted to take while I was working on writing a blog post.",
"owner": "peter"
}'

</pre>

= React =
[https://www.cloudsavvyit.com/9490/how-to-dockerise-a-react-app/ How to Dockerise A React App]

= Java and GlassFish =
[https://www.howtoforge.com/how-to-install-glassfish-application-server-with-nginx-reverse-proxy-on-debian-12 How to Install GlassFish Application Server with Nginx Reverse Proxy on Debian 12]

= Redis =
https://hub.docker.com/_/redis/

[https://github.com/metacran/metacranweb Web pages for metacran]

[https://markheath.net/post/exploring-redis-with-docker Exploring Redis with Docker]

[http://collabnix.com/running-redis-inside-docker-container-on-jetson-nano/ Redis running inside Docker container on NVIDIA Jetson Nano], [https://redis.io/topics/ARM Redis is ideal for IoT and Embedded devices for several reasons].

= Laravel =
[https://www.howtoforge.com/tutorial/dockerizing-laravel-with-nginx-mysql-and-docker-compose/ Dockerizing Laravel with Nginx MySQL and Docker Compose on Ubuntu 18.04 LTS]

= phpMyAdmin =
* https://hub.docker.com/r/phpmyadmin/phpmyadmin/. The docker-compose.yml file works instantly.
* [http://omarghader.github.io/docker-tutorial-phpmyadmin-and-mysql-server/ phpMyAdmin and MySQL server]

<syntaxhighlight lang='bash'>
docker run --name mysqlphp -e MYSQL_ROOT_PASSWORD=0000 -d mysql
docker run --name myadmin -d --link mysqlphp:db -p 8080:80 phpmyadmin/phpmyadmin
</syntaxhighlight>

Now go to your browser , tap http://localhost:8080 and login with root/0000.

'''ERROR''' mysqli_real_connect(): The server requested authentication method unknown to the client [caching_sha2_password]

The solution can be found [https://stackoverflow.com/questions/49948350/phpmyadmin-on-mysql-8-0 here]. After the change, I can log in phpMyAdmin.
<syntaxhighlight lang='bash'>
docker exec -it mysqlphp bash

mysql -u root -p0000

ALTER USER root IDENTIFIED WITH mysql_native_password BY '0000';

exit
exit
</syntaxhighlight>

= MagicMirror =
https://github.com/MichMich/MagicMirror/blob/master/README.md#docker

== Mail/smtp server ==
* [https://www.msn.com/en-us/news/technology/how-to-set-up-your-own-secure-email-server/ How to Set Up Your Own Secure Email Server] 2021-11
* [https://jzweig.com/blog/setup-your-own-email-server-with-docker/ Setup Your Own Email Server with Docker]
* [https://petermeissner.de/blog/2020/09/07/web-send-mail-windows/ Sending Emails with {curl} and Docker]
** https://hub.docker.com/r/bytemark/smtp/

= Mediawiki =
<ul>
<li>https://www.mediawiki.org/wiki/Docker
<li>https://hub.docker.com/_/mediawiki/ or (better) https://docs.docker.com/samples/library/mediawiki/. The Dockerfile is based on [https://hub.docker.com/_/php/ jessie]. 
<li>bitnami/mediawiki (Verified but too complicated, 1M+)
<li>https://hub.docker.com/r/ubcctlt/mediawiki (10M+)
<li>[https://kindalame.com/2020/11/25/self-hosting-mediawiki-with-docker/ Hosting Your Own Wiki With MediaWiki and Docker] Nov 2020. The instruction is easy to follow.
* In mediawiki set up we page, we need to enter 'database' for the Database host 
* The database information we entered will go to 'LocalSettings.php' file. But the name of wiki, administrator user name, password will go to the database.
* the instruction for the 'extensions' part seems too much. We just need to mount local 'extensions' to container's '/var/www/extensions' folder.
* Remember to run 'docker-compose down && docker-compose up -d' after we modify something
<li>[https://www.jianshu.com/p/8de371558ef6 docker搭建mediawiki]
<li>https://github.com/kristophjunge/docker-mediawiki
<li>[https://jzweig.com/blog/setup-mediawiki-and-postgres-with-docker/ Setup MediaWiki and Postgres with Docker] (based on simplyintricate/mediawiki, works on Mint). Visit http://localhost:8080 to see the result.
<pre>
$ ls -l ~/wiki_root
total 24
drwxr-xr-x 3 root     root     4096 Jul 10 10:09 data
drwxrwxr-x 3 brb      brb      4096 Jul 10 09:23 db
drwxrwxr-x 2 www-data www-data 4096 Jul 10 09:23 extensions
drwxrwxr-x 2 www-data www-data 4096 Jul 10 09:23 images
-rw-rw-r-- 1 www-data www-data 4152 Jul 10 11:12 LocalSettings.php
</pre>
</li>
<li>[https://github.com/besnik/tutorials/tree/master/docker-mediawiki Running Mediawiki as Docker container] (based on synctree/mediawiki which is not updated anymore, works tested on GalliumOS)
* Follow [https://github.com/besnik/tutorials/tree/master/docker-mysql Run MySql inside docker container] first. 1. Setup host to store configuration, data and dumps. The 'dumps' and 'initdb.d' folders are optional 2. Override default mysql configuration 3. Executing scripts and sql on container startup (optional) 4. Starting mysql container 
* Visit http://IP_address:8080 to see the mediawiki page running on Docker
<pre>
brb@galliumos:~$ tree mysql
mysql
├── conf.d
│   └── mysql.cnf
├── data
│   ├── auto.cnf
│   ├── ca-key.pem
│   ├── ca.pem
│   ├── client-cert.pem
│   ├── client-key.pem
│   ├── ib_buffer_pool
│   ├── ibdata1
│   ├── ib_logfile0
│   ├── ib_logfile1
│   ├── ibtmp1
│   ├── mediawiki [error opening dir]
│   ├── mysql [error opening dir]
│   ├── performance_schema [error opening dir]
│   ├── private_key.pem
│   ├── public_key.pem
│   ├── server-cert.pem
│   ├── server-key.pem
│   ├── sys [error opening dir]
│   └── wikidb [error opening dir]
├── dumps
└── initdb.d

9 directories, 15 files

brb@galliumos:~$ tree -L 2 mediawiki/
mediawiki/
├── config
│   └── LocalSettings.php
├── extensions
│   ├── Cite
│   ├── ConfirmEdit
│   ├── Gadgets
│   ├── ImageMap
│   ├── InputBox
│   ├── Interwiki
│   ├── LocalisationUpdate
│   ├── Nuke
│   ├── ParserFunctions
│   ├── PdfHandler
│   ├── Poem
│   ├── README
│   ├── Renameuser
│   ├── SpamBlacklist
│   ├── SyntaxHighlight_GeSHi
│   ├── TitleBlacklist
│   └── WikiEditor
└── images
    └── README

19 directories, 3 files
</pre>
</li>
<li>https://linuxconfig.org/mediawiki-easy-deployment-with-docker-container (based on linuxconfig/mediawiki)
<li>http://collabnix.com/how-to-setup-mediawiki-in-seconds-using-docker/ (based on appcontainers/mediawiki)
<li>[https://www.packtpub.com/books/content/isolated-mediawiki-setup-raspberry-pi-using-docker-part-1 Isolated MediaWiki Setup on the Raspberry Pi using Docker, Part 1]
</ul>

== BookStack ==
[https://www.bookstackapp.com/ BookStack] is a simple, self-hosted, easy-to-use platform for organising and storing information.

https://github.com/solidnerd/docker-bookstack

= Books =
== Audio Books ==
* [https://www.audiobookshelf.org/ audiobookshelf] (Self-Hosted Audible Alternative)
* [https://www.howtogeek.com/10-docker-containers-every-homelabber-should-run/ 10 Docker Containers Every Homelabber Should Run]

= HDHomeRun =
== tvheadend ==
<ul>
<li>docker-compose.yml. See [https://docs.linuxserver.io/images/docker-tvheadend/ linuxserver/tvheadend]. Open http://localhost:9981 .
<pre>
services:
    tvheadend:
        container_name: tvheadend
        environment:
            - PUID=1000
            - PGID=1000
            - TZ=Etc/UTC
        network_mode: host
        volumes:
            - ./data:/config
            - ./recordings:/recordings
        restart: unless-stopped
        image: lscr.io/linuxserver/tvheadend:latest
</pre>
<li>tvheadend setup. [https://www.youtube.com/watch?v=6Dgjn1IKrFM TVheadend and HDHomeRun using IPTV inputs]. 
<li>[https://www.youtube.com/watch?v=2Y-E4sQSb94 How to configure tvheadend server].
<li>[https://www.youtube.com/watch?v=Y4gnJRgMB9s How to install Tvheadend server on $40 Android box running Linux]. The configuration allows to scan channels on HDHomeRun.
</ul>

= Media server =

== Jellyfin ==
* https://hub.docker.com/r/jellyfin/jellyfin
* [https://youtu.be/psHLgVzjLhY Jellyfin Update - An amazing, open source, and self hosted media server alternative to Plex or Emby] (video)
* https://docs.linuxserver.io/images/docker-jellyfin (works)
** [https://www.addictedtotech.net/install-jellyfin-as-a-raspberry-pi-media-server/ Install Jellyfin As A Raspberry Pi Media Server – Episode 29]
** https://github.com/linuxserver/docker-jellyfin
* [https://jellyfin.org/downloads/clients/ Official clients]
* [https://youtu.be/aY732cSkopU ULTIMATE Jellyfin Guide - Hardware Acceleration, Codecs (PART 2) ]
* Problems:
** [https://www.reddit.com/r/jellyfin/comments/rf0taf/best_way_to_update_your_library_when_you_make/ Best way to update your library when you make changes to existing files?]. Answer: (manual) Settings - Dashboard - Libraries - Libraries - Scan all libraries, (automatic) scheduled tasks - scan media library (every 12 hour).
** My (downloaded) videos got different video titles.
* Split a large file
** If I already have 3 videos named "Video-part1.mp4", "Video-part2.mp4" and "Video-part3.mp4" (eg coming from DashCam), Jellyfin is smart enough to merge these 3 and shows only one video.
** Or we can use the commands '''ffmpeg''' , which would split the video at 30-minute intervals (1800 seconds) into 3 files : '''ffmpeg -i input.mkv -map 0 -c copy -f segment -segment_times 0,1800,3600 output%03d.mkv'''. 
*** output001.mkv: Contains the first 30 minutes of the video (0 to 1800 seconds).
*** output002.mkv: Contains the next 30 minutes of the video (1800 to 3600 seconds).
*** output003.mkv: Contains the remainder of the video (from 3600 seconds to the end).

* [https://www.howtogeek.com/5-reasons-to-run-plex-and-jellyfin-together/ 5 Reasons to Run Plex and Jellyfin Together]

== Youtube downloader ==
<ul>
<li>[https://www.reddit.com/r/selfhosted/comments/ufxouk/download_youtube_videos_host_locally/ Download YouTube videos, host locally?]
<li>[https://github.com/alexta69/metube MeTube],
<syntaxhighlight lang='sh'>
mkdir /tmp/downloads # O.W. /tmp/downloads generated by root cannot be written
docker run -d -p 8081:8081 \
  -e DELETE_FILE_ON_TRASHCAN=true \
  -v /tmp/downloads:/downloads \
  --restart always \
  alexta69/metube
# http://localhost:8081
</syntaxhighlight>
The following example value for "YTDL_OPTIONS" embeds English subtitles and chapter markers (for videos that have them), and also changes the permissions on the downloaded video and sets the file modification timestamp to the date of when it was downloaded (oudated. see examples on 
[https://github.com/yt-dlp/yt-dlp?tab=readme-ov-file#usage-and-options yt-dlp] about the current options).
{{Pre}}
docker run -d -p 8081:8081 \
  -v /tmp/downloads:/downloads \
  -e YTDL_OPTIONS='{"writesubtitles":true,"subtitleslangs":["en","-live_chat"],"updatetime":false,"postprocessors":[{"key":"Exec","exec_cmd":"chmod 0664","when":"after_move"},{"key":"FFmpegEmbedSubtitle","already_have_subtitle":false},{"key":"FFmpegMetadata","add_chapters":true}]}' \
  --name metube \
  alexta69/metube
</pre>
<li>Chapters and subtitles: 
* Testing video: [https://www.youtube.com/watch?v=yG8sFwBISVU Macha Galette]. 
* In VLC, subtitle is available under "Subtitle" -> "Sub Track" -> "English". The subtitle can be extracted from the downloaded webm files using <syntaxhighlight lang='sh' inline>ffmpeg -i filename.webm -map 0:s:0? subs.srt</syntaxhighlight>. If a video's subtitle is auto-generated by Youtube, then there is no subtitle embedded in the downloaded webm files.
* In VLC, chapters is available under "Playback" -> "Chapter"
<li>[https://github.com/yt-dlp/yt-dlp yt-dlp]
<li>[https://github.com/Tzahi12345/YoutubeDL-Material YoutubeDL-Material]
</ul>

== Airsonic media server ==
https://airsonic.github.io/download/

My comment: 
* Added mp3/mp4 files are not recognized.
* Cannot play by web browsers
* Special clients are needed:(

== Plex ==
* [https://github.com/plexinc/pms-docker Official Docker container for Plex Media Server]
* https://hub.docker.com/r/linuxserver/plex/
* Live tv subtitles/captions: Server -> Settings -> Languages -> Subtitle mode -> Always enabled -> Save Changes.
* [https://www.plex.tv/plex-pass/ Plex Pass] subscription
** [https://support.plex.tv/articles/225877347-live-tv-dvr/ Live tv DVR]
** [https://support.plex.tv/articles/115002178853-using-hardware-accelerated-streaming/ Using Hardware-Accelerated Streaming]
<pre>
---
services:
  plex:
    image: lscr.io/linuxserver/plex:latest
    container_name: plex
    network_mode: host
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=US/Eastern
      - VERSION=docker
      - PLEX_CLAIM= #optional
    volumes:
      - /tmp/plex/library:/config
      - /tmp/plex/tvseries:/tv
    devices:
      - /dev/dri:/dev/dri
    restart: unless-stopped
</pre>

== Sonarr, Radarr, Prowlarr ==
* [https://www.youtube.com/watch?v=LD8-Qr3B2-o Make Automated Torrent Media Server with Emby, Sonarr, Radarr, Prowlarr, and qBittorrent on Windows!]
* [https://www.youtube.com/watch?v=zfYthZrDpVU How to install and configure Sonarr]

== MoonTV ==
https://github.com/senshinya/MoonTV

= DNS server =
[https://linuxconfig.org/protecting-your-privacy-with-firefox-on-linux#h4-1-private-dns Private DNS server container]

[https://www.howtoforge.com/tutorial/how-to-deploy-a-dynamic-dns-server-with-docker-on-debian-10/ How to Deploy a Dynamic DNS Server with Docker on Debian 10]

= Update DNS entries: ddclient =
* https://hub.docker.com/r/linuxserver/ddclient/
* https://github.com/linuxserver/docker-ddclient

= WireHole =
* https://github.com/IAmStoxe/wirehole
* [https://youtu.be/DOJ39lyx6Js WireHole: WireGuard, Pi-Hole and Unbound in Docker] (video)

= Speed test =
* [[Benchmark#OpenSpeedTest|OpenSpeedTest]]
* [https://github.com/alexjustesen/speedtest-tracker Speedtest Tracker] (3.7k)
** [https://www.howtogeek.com/this-docker-container-turned-my-nas-into-an-internet-performance-dashboard/ This Docker Container Turned My NAS Into an Internet Performance Dashboard]

* https://myspeed.dev/, https://github.com/gnmyt/myspeed (1.4k)
** http://localhost:5216. I need to open the page in incognito mode when using SSH local forwarding.
** For remote access, use '''ssh -L 5216:localhost:5216 username@remoteserver'''
** Visit http://localhost:5216 to access the webpage
** Settings -> Manage Storage -> Speedtest -> Export tests.
* [https://www.youtube.com/watch?v=tBJmhgn3ZOM MySpeed: Speedtest Automation Made Simple!]

= Pi-hole =
<ul>
<li>https://hub.docker.com/r/pihole/pihole/, https://github.com/pi-hole/docker-pi-hole
<li>On Boox Note Air, Settings - Wireless - SSID. 
* Proxy = None (default)
* IP Settings - Static. Enter desired IP address & Gateway & DNS1 & DNS2.
<li>[https://pimylifeup.com/raspberry-pi-pi-hole/ Raspberry Pi Pi-Hole]: A Network Wide Ad-blocker
<li>[https://homenetworkguy.com/how-to/install-pihole-on-raspberry-pi-with-docker-and-portainer/ Install Pi-hole on a Raspberry Pi with Docker and Portainer]
<li>[https://pimylifeup.com/pi-hole-docker/ Running Pi-Hole as a Docker Container]. Ubuntu.
* (Ubuntu) The command to disable the [https://wiki.archlinux.org/title/Systemd-resolved Systemd-Resolve] Service (Network Name Resolution manager) seems to be outdated. '''sudo systemctl stop systemd-resolve''' returns a message ''Failed to stop systemd-resolve.service: Unit systemd-resolve.service not loaded.''
* It looks ''sudo systemctl status systemd-resolved'' still works in Ubuntu 22.04
* Before deploying pi-hole, run the following commands ([https://jeremygotcher.com/2022/12/28/ubuntu-22-04-docker-portainer-pi-hole/ Ubuntu 22.04, Docker, Portainer, Pi-Hole]):
<pre>
sudo systemctl stop systemd-resolved
sudo systemctl disable systemd-resolved
</pre>
<li>[https://www.how2shout.com/linux/how-to-install-pi-hole-on-docker-network-wide-ad-blocking/ How to install Pi-hole on Docker – Network-wide Ad Blocking]
<pre>
sudo docker volume create etc-pihole
sudo docker volume create etc-dnsmasq.d
sudo docker run -d --name pihole \
  -p 53:53/tcp -p 53:53/udp -p 67:67 -p 80:80 -p 443:443 \
  -e TZ="Asia/Kolkata"  \
  -v etc-pihole:/etc/pihole/ \
  -v etc-dnsmasq.d:/etc/dnsmasq.d/ \
  --dns=127.0.0.1 --dns=1.1.1.1 --restart=unless-stopped \
  --hostname pi.hole \
  -e VIRTUAL_HOST="pi.hole" \
  -e ServerIP="127.0.0.1" \
  pihole/pihole:latest
</pre>
</ul>

= Authentication =
== Authelia ==
* https://hub.docker.com/r/authelia/authelia Authelia is an open-source authentication and authorization server providing two-factor authentication and single sign-on (SSO) for your applications via a web portal
* [https://youtu.be/5KtbmrUwYNQ Authelia - Free, Open Source, Self Hosted authorization and authentication for your web applications] and [https://shownotes.opensourceisawesome.com/authelia-authentication/ Notes]
* [https://helgeklein.com/blog/samba-file-server-web-access-through-filebrowser-with-sso-https/ Samba File Server: Web Access Through Filebrowser With SSO & HTTPS]
* [https://www.youtube.com/watch?v=4UKOh3ssQSU Additional Self-Hosted Security with Authelia on NGINX Proxy Manager] (video)

== Authentik ==
* https://goauthentik.io/
* [https://www.youtube.com/watch?v=enwFWELCYJo Single Sign On With OAuth2.0 - Authentik Is AWESOME!]
* [https://www.youtube.com/watch?v=Nh1qiqCYDt4 Authentik - Application Setup | Nginx Proxy Manager | (Docker/Compose)]
* [https://www.youtube.com/watch?v=KlDJ4K45M_o Authentik - open source, self hosted authentication system with OIDC, SAML, and more...] and [https://wiki.opensourceisawesome.com/books/authentik/page/install-and-setup-authentik written notes].

= Whoogle =
https://github.com/benbusby/whoogle-search

= Backup =
== Duplicati ==
* https://hub.docker.com/r/duplicati/duplicati/
* [https://youtu.be/--lYljZzrCQ Backup Your Docker Server NOW! - Setup and Configure Duplicati] (video)

= Python =
* [https://www.docker.com/blog/containerized-python-development-part-1 Containerized Python Development – Part 1], 
* [https://www.docker.com/blog/containerized-python-development-part-2/ Part 2]
** Managing Project Configuration with Docker Compose
** Compose file
** Best practices for writing Compose files
* [https://www.docker.com/blog/how-developers-can-get-started-with-python-and-docker/ How Developers Can Get Started with Python and Docker]

== Conda ==
* Prebuilt conda image: https://hub.docker.com/r/continuumio/miniconda3, https://hub.docker.com/r/continuumio/anaconda3/
* Conda-Forge Miniforge Images: https://hub.docker.com/r/condaforge/miniforge3
<pre>
# Pull the image
docker pull continuumio/anaconda3

# Run a container from the image
docker run -it continuumio/anaconda3 /bin/bash

# Inside the container, create a new Conda environment
conda create -n myenv python=3.8

# Activate the environment
conda activate myenv

# Install packages
# conda install numpy pandas
conda install numpy=1.21.2 pandas=1.3.3

# Verify installation
conda list

# Remove packages
conda remove numpy

# Run your application
python myscript.py

# Exit the container
exit

# List running containers
docker ps

# Stop a container
# docker stop <container_id>

# Remove a container
# docker rm <container_id>

# Commit changes to a new image
# docker commit <container_id> mynewimage

# Push the new image to a registry
# docker push mynewimage
</pre>

= Python Jupyter including R =
* [https://github.com/jupyter/docker-stacks Jupyter Docker Stacks], 
* https://registry.hub.docker.com/r/jupyter/datascience-notebook/
* [https://youtu.be/UXxUcZDSNwA How to customize the jupyter/datascience-notebook container with docker-compose]. Change the $PWD below for your case.
<pre>
docker run --rm -p 8888:8888 \
      -e JUPYTER_ENABLE_LAB=yes \
      -v "$PWD":/home/jovyan/work \
      --name jupyter \
      jupyter/datascience-notebook:r-4.3.1
</pre>
Follow the screen output to access the app by going to http://IP:8888/?token=XXXXXX. This will take care of the authentication problem. 

If we use 'docker compose up -d' method below, we need to use 'docker logs jupyter' to get the URL which includes the token password.
<pre>
version: '3.3'
services:
    datascience-notebook:
        ports:
            - '8888:8888'
        environment:
            - JUPYTER_ENABLE_LAB=yes
        volumes:
            - '"$PWD":/home/jovyan/work'
        container_name: jupyter
        restart: unless-stopped
        image: 'jupyter/datascience-notebook:r-4.3.1'
</pre>

This includes python3, Julia 1.0.0 and R. However, the R version is pretty old if we don't specify the tag.

Also the method does not work on arm64. ''WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested.''

Keyboard shortcuts: 
* '''ctrl+Enter''' to run. 
* '''alt+Enter''' to run & insert a cell below. 
* '''shift+Enter''' to run and shift to a cell below.
* Esc: command mode
* Enter: edit mode

Note by default the ipynb files are saved to /home/jovyan instead of /home/jovyan/work directory. So it's better to click the "work" icon on the LHS of the file panel in order to change the working directory to "work".

= Calibre =
* https://hub.docker.com/r/linuxserver/calibre. It works on x86 and it can be run as a service so we don't need to keep the app open like the Desktop version. 
** See the [https://github.com/linuxserver/docker-calibre/blob/master/Dockerfile Dockerfile] and [https://github.com/linuxserver/docker-baseimage-guacgui docker-baseimage-guacgui] and [https://guacamole.apache.org/ Apache Guacamole]. 
** The ARM variants can be built on x86_64 hardware using multiarch/qemu-user-static. See https://github.com/multiarch/qemu-user-static.
* [https://github.com/janeczku/calibre-web Calibre-Web] is a web app providing a clean interface for browsing, reading and downloading eBooks using a valid Calibre database.

= RSS =
* https://hub.docker.com/r/freshrss/freshrss/
* [https://hub.docker.com/r/linuxserver/freshrss/ FreshRSS]

= Read it later/Pocket =
<ul>
<li>[https://lifehacker.com/tech/mozillas-pocket-app-is-shutting-down How to Export Your Saved Articles Before Pocket Shuts Down for Good]
<li>[https://www.androidpolice.com/pocket-is-dead-here-are-alternatives-to-save-links-instead/ Pocket is dead: Here are 6 alternatives to save links instead]
<li>[https://wallabag.org/ Wallabag]
* https://hub.docker.com/r/wallabag/wallabag
* (YT) [https://www.youtube.com/watch?v=OoTMoKtSOaI Wallabag - Save Web Pages for Later on Docker]

<li>(Not self-hosted) [https://raindrop.io/ Raindrop.io] and [https://www.instapaper.com/ Instapaper].
<li>[https://www.linuxlinks.com/karakeep-self-hostable-bookmark-everything-app/ Karakeep is a self-hostable bookmark-everything app]
<li>[https://github.com/omnivore-app/omnivore Omnivore]

</ul>

= Home Assistant =
* [https://www.youtube.com/watch?v=42gopfIrPBY&list=PLGk2on7ccZOMMdaljjX8jeDpWhJGPzrcs&index=1&t=331s Install Proxmox and virtualize Home Assistant]
* [https://www.makeuseof.com/build-cheap-wireless-security-camera/ How to Build a $10 Wireless IP Security Camera for Your Home]

= Password manager =

== Settings ==
[https://www.makeuseof.com/important-password-manager-settings/ These Are the 7 Password Manager Settings That Actually Matter]

== Bitwarden ==
* [https://www.youtube.com/watch?v=FSme38DPnak 一键部署 Bitwarden 密码管理器！完全开源，支持跨平台使用，100% 安全又可靠，密码自己掌控]
* [https://youtu.be/mq7n_0Xs1Kg Vaultwarden - Open Source, self hosted backend for the Bitwarden password manager] (video)

== KeeWeb: password manager compatible with KeePass ==
https://github.com/keeweb/keeweb

== Padloc: cloud-based password manager ==
* Padloc is a cloud-based password management solution that allows you to access and use your saved passwords across multiple platforms. 
* [https://www.howtoforge.com/how-to-install-padloc-password-manager-on-rocky-linux-8/ How to Install Padloc Password Manager on Rocky Linux 8]

= Share passwords =
[https://youtu.be/ImvOmI9El2k Share Password and Secrets Securely! Self-Destructing Messages with PassED (Docker)]

= Flask =
[https://www.howtoforge.com/dockerizing-flask-application-using-docker-on-debian-10/ Dockerizing Flask Application Using Docker on Debian 10]

= ONLYOFFICE =
* https://www.howtoforge.com/tutorial/how-to-install-onlyoffice-8.9.0-with-docker-on-ubuntu/
* https://www.howtoforge.com/tutorial/how-to-update-onlyoffice-to-version-95-with-docker/ This involves backing up and restoring MYSQL data.

= Gitlab =
* https://docs.gitlab.com/omnibus/docker/
* https://hub.docker.com/r/gitlab/gitlab-ce/
* [https://www.howtoforge.com/tutorial/how-to-install-gitlab-server-with-docker-on-ubuntu-1804/ How to Install Gitlab Server with Docker on Ubuntu 18.04 LTS]
* [https://www.howtoforge.com/how-to-install-gitlab-with-docker-on-ubuntu-2004/ How to Install GitLab with Docker on Ubuntu 20.04 LTS]

= NAS & Docker =
http://www.ithome.com.tw/tech/96500

Some examples
* GetLab專案管理工具
* Jenkins開發版本管理工具

= Memo/note =
* https://github.com/usememos/memos, [https://youtu.be/uxSV8UY5x5Y Memos: The EASY Way to Take Notes]

= Draw.io for diagrams and more =
<ul>
<li>https://github.com/jgraph/drawio/tree/master/etc/docker
<pre>
docker run -d --restart=unless-stopped \
   --rm --name="draw" -p 8080:8080 \
   -p 8443:8443 jgraph/drawio
</pre>
<li>To allow to save to devices, the app and the file have to be on the same machine.
<li>It is super easy to install draw.io in Nextcloud (just a few clicks). It is very natural to save the file in the Nextcloud storage.
</ul>

= Internet Archive: ArchiveBox =
* [https://ostechnix.com/self-host-internet-archive-with-archivebox/ How To Self-host Your Own Internet Archive With ArchiveBox In Linux]
* [https://www.maketecheasier.com/turn-raspberry-pi-into-private-internet-archive/ How I Turned My Raspberry Pi Into a Private Internet Archive]

== Linkwarden ==
[https://github.com/linkwarden/linkwarden Linkwarden] Bookmark Preservation for Individuals and Teams

= Run a benchmark program on ARM devices =
* [http://www.element14.com/community/people/markfink/blog/2015/02/05/using-docker-on-beaglebone-black?CMP=SOM-EUROPE-MFINK-BBBlack Beaglebone black] as an example. More device examples can be found on [http://www.testing-software.org/internet_of_things.html http://www.testing-software.org/].

= Cheat.sh =
https://github.com/chubin/cheat.sh#docker

= Set up a Mastodon Instance on Linux =
* https://joinmastodon.org/
* [http://www.makeuseof.com/tag/social-network-set-mastodon-instance-linux/ Your Own Social Network: How to Set Up a Mastodon Instance on Linux]
* [https://youtu.be/w_Xgw-UgcDI 3 Amazing Mastodon Clients for you to use to access a truly open social media platform & Fediverse]
* [https://www.usatoday.com/story/tech/2022/11/16/twitter-alternative-mastodon-social-network/8303119001/ What is Mastodon? What to know about the decentralized site some see as a Twitter alternative]
* [https://www.nature.com/articles/d41586-022-03668-7 Should I join Mastodon? A scientists’ guide to Twitter’s rival]

= Bioinformatics tools (Tophat, BWA, et al) =
https://github.com/dceoy/docker-bio

= cbioportal =
* Docker
** [https://docs.cbioportal.org/2.1.1-deploy-with-docker-recommended/docker Deploy with Docker]
** https://github.com/cBioPortal/cbioportal-docker-compose includes Connect to the database, Run different cBioPortal version, Change the heap size.
** https://github.com/cBioPortal/cbioportal
* https://groups.google.com/g/cbioportal
* docker-compose up is OK, but it requires me to restart the container (I wasn't instructed to do that. Documents need to improve).
<ul>
<li>Import study does not work if we use the docker-compose method. It works if we use '''docker exec -it CONTAINER bash'''. 
{{Pre}}
[brb@localhost cbioportal-docker-compose]$ docker-compose run cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o
Creating cbioportal-docker-compose_cbioportal_run ... done
Starting validation...

CRITICAL: -: No meta files found in study/lgg_ucsf_2014/. Please make sure the directory is the path to the folder containing the files.
ERROR: -: Cancer type needs to be defined for a study. Verify that you have a study file and have defined the cancer type correctly.
ERROR: -: No valid study file detected
</pre>
See also https://github.com/cBioPortal/cbioportal/issues/7972
</li>
<li>The version number shown on http://localhost:8080 is v3.4.17 (see [https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/.env .env] variable) but the https://www.cbioportal.org/ website shows v3.5.3 (same as the current release version on [https://github.com/cBioPortal/cbioportal Github] & [https://hub.docker.com/r/cbioportal/cbioportal/tags Docker hub])  </li>
<li>The 2nd field on the 1st row of '''data_cancer_type.txt''' contains the study name (blue color) shown on website </li>
<li>'''meta_study.txt ''' contains the study name (black color) shown on website </li>
<li>study_es_0 (breast, contains mRNA expression) and study_es_3 can be imported successfully when I use '''docker-compose exec -it CONTAINER bash''' and follow [https://docs.cbioportal.org/2.1.2-deploy-without-docker/load-sample-cancer-study Load sample cancer study].</li>
<li>lgg_ucsf_2014 study (brain, CNA) should use the correct path '''docker-compose run cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/lgg_ucsf_2014/ -o'''  </li>
<li>I have tested on CentOS 7 and Ubuntu 20.04 on KVM/QEMU w/ 2 cores, 2/4GB memory, 25GB storage. I can use host's terminal and browser for interaction (i.e. no VNC/Spice server needed).</li>
<li>[http://blog.thehyve.nl/blog/gene-panels-cbioportal-patient-view Gene panels in the cBioPortal patient view] 2020-01-07, and other blogs related to cbioportal from '''thehyve'''.
<ul>
<li>[http://blog.thehyve.nl/blog/simple-data-loading-into-cbioportal-with-docker Simple data loading into cBioPortal with Docker (Updated 2019)] </li>
<li>[http://blog.thehyve.nl/blog/cbioportal-setup-made-easy-using-docker cBioPortal setup made easy using Docker (Updated 2019)] </li>
</ul>
</li>
</ul>

= GIVE - Genomic Interactive Visualization Engine =
https://github.com/Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine/blob/master/tutorials/GIVE-Docker.md

= GeneTEFlow: Analysing gene and transposable elements expression from RNA-Seq data =
[https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232994 GeneTEFlow]: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. [https://github.com/zhongw2/GeneTEFlow Source code].

= [https://www.elastic.co/ Elastic Search] =
* https://www.elastic.co/guide/en/elasticsearch/reference/current/docker.html
* https://docs.docker.com/samples/library/elasticsearch/
* https://github.com/triestpa/guttenberg-search

= Webpage monitor tools =
* [https://github.com/statping/statping/wiki/Features statping]
* [https://github.com/dgtlmoon/changedetection.io changedetection.io], [https://www.reddit.com/r/selfhosted/comments/wsalyz/changedetectionio_the_selfhosted_website_change/ releases version v0.39.18]
** [https://youtu.be/SmUDirCSaoE ChangeDetection.io with Browser Agent Support in Docker]
* [https://www.makeuseof.com/best-website-change-detection-tools/ The 7 Best Free and Paid Website Change Detection Tools]

= AI =
== Grammarly alternative == 
[https://www.howtogeek.com/run-your-own-private-grammarly-clone-using-docker-and-languagetool/ Run Your Own Private Grammarly Clone Using Docker and LanguageTool]

= CasaOS =
* https://casaos.io/, [https://wiki.casaos.io/en/guides Wiki] (Very limited)
* https://blog.casaos.io/ Blog and new release announcement
* [https://docs.zimaboard.com/docs/Self-Deploying-Applications.html Self-Deploying-Applications] from Zimaboard.
* I installed CasaOS in Proxmox using Debian 12 LXC. I allocated 40GB space and 4GB ram. The memory can be increased without a need to shut down the LXC.
* Files app is similar to NextCloud but it can connect to cloud storage like Google Drive, Dropbox and OneDrive. It can also connect to other network storage something like smb://192.168.1.1
* I guess we are supposed to use CasaOS in a full screen model. The backward button in the browser will possibly quit CasaOS.
* Portainer, Uptime Kuma, Wireguard Easy are some of apps in the App Store.
* CasaOS can expand their App Store. 
** Custom installer is another option; we can use Docker Compose or Docker CLI.
** "Add Source". [https://awesome.casaos.io/content/3rd-party-app-stores/list.html Store list]. After I copy/paste CasaOS-LinuxServer-AppStore '''https://casaos-appstore.paodayag.dev/linuxserver.zip''' and click "Add +" button it immediately shows 226 apps. That is cool! It includes Firefox, Chromium, Opera. I installed FF but when I use the web interface of FF on my Android tablet, I could not scroll. FreshRSS not working on my tablets. Firefox and Chromium are hard to use on my tablet.
** Apps are using ports other than 80. Clicking on an app (eg Snapdrop was changed to use port 88 instead of 80) sometimes opened a tab with a port 80. So the launching is not successfully. We need to click on each app's Settings and find out what the port it uses and modify the port on the Web UI field and 'Save'.
** Kasm not working.
** Snapdrop. I can't see other devices? [https://docs.linuxserver.io/images/docker-pairdrop/ pairdrop] from linuxserver.io works.
** OpenSpeedTest & librespeed/speedtest works but gave quite different results than speedtest.net
** [https://www.helpwire.app/blog/rdesktop-linux/ Rdesktop]. It is [https://youtu.be/jt_C3cStfAA?si=Mp-4UpV30Gn3lKVw&t=22 adding a desktop environment to your server]. So the IP should be IP:3389 when we use Remmina for example. The username/password is abc/abc. For example, I allocate 40GB to CasaOS and the remote desktop will show 40GB disk space for the server. The desktop includes the Chromium browser. We can connect to internet using the Chromium browser.
** [https://docs.linuxserver.io/images/docker-webtop/ Webtop] ([https://wiki.opensourceisawesome.com/books/webtops-for-remote-sessions/page/webtops-linux-desktops-in-docker video]) is based on KasmVNC. Webtops is a project where you can setup a variety of Linux desktops, with a variety of Desktop Environments in Docker, and access them through a web browser! The screen/desktop is synchronized across devices. So we can use our tablet device as a monitor and our mouse and keyboard are still connected to our desktop computer. Interesting! But no internet connection? The font size on the desktop changes with the connected devices. The default distro is Arch Linux.
** AdGuard: when I installed it, '''the default port for dashboard is 80'''. I changed it to 3000. But after the setup, the port 3000 is not working. Check the setting from CasaOS, it shows 3001. So the change of port in the initial set up was not taken (I ssh into the server and use '''ss''' to check open ports) though admin account was saved. The port 3001 is actually working. It works when I tested on a Android tablet (use only AdGuard IP as the only DNS, not including 1.1.1.1 or else). See [https://youtu.be/u9ylq5Gry_A?si=THSqnh84_VtdFhLv Adguard Home Installed on Docker] video for AdGuard setup. 
** ddclient, Duckdns, Duplicati, [https://github.com/healthchecks/healthchecks healthchecks] (A watchdog for your cron jobs).
* [https://icewhale.community/t/casaos-tailscale-seamless-home-network-integration-remote-access-to-your-data/84 CasaOS+Tailscale: Seamless Home Network Integration + Remote access to your data]