Docker Applications

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Homelab

Top/best

Templates

App store

Tipi

Dockerizing Compiled Software

Crontab

Install macOS

Raspberry Pi servers based on Docker

Data Science

Data Science

Illumina BaseSpace

Bioinformatics analyses

Cloud provider

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

Dashboard

Dashy

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

Glance

Homepage

https://github.com/gethomepage/homepage

Flame

https://github.com/pawelmalak/flame

Homer

Uptime Kuma

heimdall

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

Dashboard for monitoring system: grafana

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 photo

Immich

PhotoPrism

ownCloud

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

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.

Nextcloud Apps

  • "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.
  • Audio Player. When I play mp3 files, the web interface does not show a progress bar:( 
    $ 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.
  • 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:) 
    # 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
    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 
    $ 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
    If we like to delete the contain and its unamed volume, run 
    $ docker stop mycloud; docker rm -v mycloud
    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)
  • draw.io. After enable it, we can click the "+" sign and choose "Diagram" to create a new diagram (*.xml).
  • 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".

Music: Navidrome

Navidrome Is the Perfect Self-Hosted Music Server for Raspberry Pi

FileRun

File manager

File browser

The original image (filebrowser/filebrowser) does not work but linuxserver's image (filebrowser/filebrowser:s6) works fine. 

$ 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

FilGator

https://filegator.io/

Seafile

Run a Linux desktop

Run a Linux desktop VM with VNC

Run Ubuntu Linux in Docker with Desktop Environment and VNC

Kasm workspaces

Distrobox

  • 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?)
    • Practical uses:
      • Running GUI Applications from Other Distros (Containers): distrobox-enter fedora-box -- firefox
      • 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.
  • Installation
  • DEB Files on Arch? Run Any App on Any Linux Distro With This Tool
  • Distrobox: Try Multiple Linux Distributions via the Terminal. The line "distrobox-export --app foliate" gives an error "cannot find any desktop files".
  • Stop Distro Hopping! Use this AWESOME tool on Linux 7/15/2023
    • Linux subsystem in another Linux
  • Testing using arch linux where packages are always updated. Refer to distrobox create doc for examples. 
    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

    Use GUI Applications from the Container 

    apt install x11-apps -y
xeyes
  • List of compatible images and container managers, Compatibility page.
  • 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
  • Change the default container manager. distrobox-create --help. 
    DBX_CONTAINER_MANAGER="docker"
  • 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.
  • BoxBuddy – graphical manager for Distrobox

Guacamole

Webtop: Linux desktop in a browser

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
  • Meet Webtops A Linux Desktop Environment In Your Browser
  • Run Linux Desktops in your Browser with Docker and Webtops! (video) and Notes
  • Default username/password is abc/abc. But we don't need to enter the password when we use "sudo".
  • Linux desktop, inside of a container, inside of a browser??? Yes. A Webtop, privileged: true is required for installing something like vscode in VM (video) and 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 Installing R Studio on Ubuntu 22.04 works for me.
$ 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

instantbox

Firewall/router/Vlan

IDE

cloud9

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

VS Code

Docker for R (r-base, rstudio)

See R Docker.

Docker for Shiny Server

  • 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 kmeans example). 
    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
  • Question: what happened if there is a new version of R or shiny-sever? 
    # 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

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). 

# 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

And check running status 

$ docker ps -a

R packages installation: packrat

Check opened ports

See What network ports are open: lsof or netstat. 

$ 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

Blog Explorer

https://github.com/nz-stefan/blog-explorer, Winners of the 2nd Annual Shiny Contest

Raspberry Pi

The Raspberry Pi 4B as a shiny server

BioContainers

CMS, blog website

Ghost

Proxy

  • Best proxy - traefik, NPM, SWAG, caddy or other?
  • swag

Nginx proxy manager

Caddy

Website analysis

Nginx

httpd/apache

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

Tomcat

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

ASP.NET

Forum

How to Install Discourse Forum with Docker on CentOS 8

Jenkins for continuous integration

MySQL

  • https://hub.docker.com/r/mysql/mysql-server/
  • 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 
    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'
    # 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)
  • How To Create And Test MySQL Database Server in Docker On Ubuntu Linux (video). Use Dockerfile.
  • MySQL Docker Containers: Understanding the basics, https://youtu.be/qJQPckRYNis?t=16m29s 
    # 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
  • Use Docker to run a typical MySQL server from Code Review Videos 
    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

Backup and restore

# 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

PostgreSQL

Jekyll

Building Jekyll Sites within VS Code Dev Containers

node.js

Dockerizing Node.js. See the code here. 


$ docker build -t my-node-app .
$ docker run -p 3000:3000 my-node-app

How To Setup Your Local Node.js Development Environment Using Docker (not working) 

$ 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"
}'

React

How to Dockerise A React App

Redis

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

Web pages for metacran

Exploring Redis with Docker

Redis running inside Docker container on NVIDIA Jetson Nano, Redis is ideal for IoT and Embedded devices for several reasons.

Laravel

Dockerizing Laravel with Nginx MySQL and Docker Compose on Ubuntu 18.04 LTS

phpMyAdmin

docker run --name mysqlphp -e MYSQL_ROOT_PASSWORD=0000 -d mysql
docker run --name myadmin -d --link mysqlphp:db -p 8080:80 phpmyadmin/phpmyadmin

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 here. After the change, I can log in phpMyAdmin. 

docker exec -it mysqlphp bash

mysql -u root -p0000

ALTER USER root IDENTIFIED WITH mysql_native_password BY '0000';

exit
exit

MagicMirror

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

Mail/smtp server

Mediawiki

  • https://www.mediawiki.org/wiki/Docker
  • https://hub.docker.com/_/mediawiki/ or (better) https://docs.docker.com/samples/library/mediawiki/. The Dockerfile is based on jessie.
  • bitnami/mediawiki (Verified but too complicated, 1M+)
  • https://hub.docker.com/r/ubcctlt/mediawiki (10M+)
  • 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
  • docker搭建mediawiki
  • https://github.com/kristophjunge/docker-mediawiki
  • Setup MediaWiki and Postgres with Docker (based on simplyintricate/mediawiki, works on Mint). Visit http://localhost:8080 to see the result. 
    $ 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
  • Running Mediawiki as Docker container (based on synctree/mediawiki which is not updated anymore, works tested on GalliumOS)
    • Follow 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
    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
  • https://linuxconfig.org/mediawiki-easy-deployment-with-docker-container (based on linuxconfig/mediawiki)
  • http://collabnix.com/how-to-setup-mediawiki-in-seconds-using-docker/ (based on appcontainers/mediawiki)
  • Isolated MediaWiki Setup on the Raspberry Pi using Docker, Part 1

BookStack

BookStack is a simple, self-hosted, easy-to-use platform for organising and storing information.

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

HDHomeRun

tvheadend

Media server

Jellyfin

Youtube downloader

  • Download YouTube videos, host locally?
  • MeTube, 
    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

    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 yt-dlp about the current options). 

    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
  • Chapters and subtitles:
    • Testing video: Macha Galette.
    • In VLC, subtitle is available under "Subtitle" -> "Sub Track" -> "English". The subtitle can be extracted from the downloaded webm files using ffmpeg -i filename.webm -map 0:s:0? subs.srt. 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"
  • yt-dlp
  • YoutubeDL-Material

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

---
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

Sonarr, Radarr, Prowlarr

DNS server

Private DNS server container

How to Deploy a Dynamic DNS Server with Docker on Debian 10

WireHole

Speed test

Pi-hole

Authelia

Whoogle

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

Backup

Duplicati

Python

Python Jupyter including R

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

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. 

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'

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

RSS

Read it later/Pocket

Omnivore

Home Assistant

Password manager

Bitwarden

KeeWeb: password manager compatible with KeePass

https://github.com/keeweb/keeweb

Padloc: cloud-based password manager

Flask

Dockerizing Flask Application Using Docker on Debian 10

ONLYOFFICE

Gitlab

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

Draw.io for diagrams and more

  • https://github.com/jgraph/drawio/tree/master/etc/docker 
    docker run -d --restart=unless-stopped \
   --rm --name="draw" -p 8080:8080 \
   -p 8443:8443 jgraph/drawio
  • To allow to save to devices, the app and the file have to be on the same machine.
  • 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.

Internet Archive

How To Self-host Your Own Internet Archive With ArchiveBox In Linux

Run a benchmark program on ARM devices

Cheat.sh

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

Set up a Mastodon Instance on Linux

Bioinformatics tools (Tophat, BWA, et al)

https://github.com/dceoy/docker-bio

cbioportal

  • Import study does not work if we use the docker-compose method. It works if we use docker exec -it CONTAINER bash. 
    [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

    See also https://github.com/cBioPortal/cbioportal/issues/7972

  • The version number shown on http://localhost:8080 is v3.4.17 (see .env variable) but the https://www.cbioportal.org/ website shows v3.5.3 (same as the current release version on Github & Docker hub)
  • The 2nd field on the 1st row of data_cancer_type.txt contains the study name (blue color) shown on website
  • meta_study.txt contains the study name (black color) shown on website
  • 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 Load sample cancer study.
  • 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
  • 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).
  • Gene panels in the cBioPortal patient view 2020-01-07, and other blogs related to cbioportal from thehyve.

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

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. Source code.

Elastic Search

Webpage monitor tools

CasaOS

  • https://casaos.io/, Wiki (Very limited)
  • https://blog.casaos.io/ Blog and new release announcement
  • 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". 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? pairdrop from linuxserver.io works.
    • OpenSpeedTest & librespeed/speedtest works but gave quite different results than speedtest.net
    • Rdesktop. It is 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.
    • Webtop 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 Adguard Home Installed on Docker video for AdGuard setup.
    • ddclient, Duckdns, Duplicati, healthchecks (A watchdog for your cron jobs).
  • CasaOS+Tailscale: Seamless Home Network Integration + Remote access to your data
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