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Docker notes

docker build -t my_shinyapp .
docker build --no-cache -t my_shinyapp .

FOR /f "tokens=*" %i IN ('docker ps -q') DO docker stop %i
docker image prune -f & docker system prune

docker exec -it heuristic_bell bash

docker ps
docker kill dd999ddde1be

docker run -p 80:3838 my_shinyapp

docker-compose up --force-recreate --build

Installation on RedHat server

Install Docker

https://www.cyberciti.biz/faq/install-use-setup-docker-on-rhel7-centos7-linux/

sudo yum remove docker docker-common docker-selinux docker-engine-selinux && docker-engine docker-ce
sudo yum install -y yum-utils device-mapper-persistent-data lvm2
sudo yum-config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo
sudo yum install docker-ce
sudo systemctl enable docker.service
sudo systemctl start docker.service

Install Docker compose

sudo yum install epel-release
sudo yum install -y python-pip
sudo pip install docker-compose

Install QC4Metabolomics

Download QC4Metabolomics.

sudo yum install docker git git-lfs
cd /opt
sudo git lfs clone https://github.com/stanstrup/QC4Metabolomics.git
cd QC4Metabolomics/
sudo chmod +x ./setup/*.sh

Setup paths.

db_path=/var/lib/QC4Metabolomics/db
config_path=/var/lib/QC4Metabolomics/config
data_path=/var/lib/QC4Metabolomics/data
sudo mkdir -p $db_path
sudo mkdir -p $config_path
sudo mkdir -p $data_path
sudo sed -i "17s|^.*source.*$|        source: ${db_path}|g" docker-compose.yml
sudo sed -i "41s|^.*source.*$|          source: ${config_path}|g" docker-compose.yml
sudo sed -i "44s|^.*source.*$|          source: ${data_path}|g" docker-compose.yml
sudo sed -i "66s|^.*source.*$|          source: ${config_path}|g" docker-compose.yml
sudo sed -i "69s|^.*source.*$|          source: ${data_path}|g" docker-compose.yml
sudo sed -i "90s|^.*source.*$|          source: ${data_path}|g" docker-compose.yml
sudo cp /opt/QC4Metabolomics/MetabolomiQCsR/inst/extdata/MetabolomiQCs.conf $config_path

Edit $config_path/MetabolomiQCs.conf

Build image and start. This can take hours.

sudo docker-compose up --force-recreate --build

Might not be needed.

systemctl enable firewalld
systemctl start firewalld

sudo firewall-cmd --add-port=80/tcp --permanent
sudo firewall-cmd --reload
sudo systemctl restart docker.service

Update

sudo git fetch --all
sudo git reset --hard origin/master

redo from "sudo chmod +x ./setup/converter_cron.sh".

TODO: make script for the fixed and an update script.

Upgrade mariaDB

Check the name of the mariaDB container

docker ps

Use the name to login to the machine:

docker exec -it qc4metabolomics-mariadb-1 bash

OR

winpty docker exec -it qc4metabolomics-mariadb-1 bash

Then upgrade the DB.

mysql_upgrade -p

Restart the container