QC4metabolomics

QC systems for metabolomics studies

Demo

Prerequisites

• Docker
• Docker compose
• Git and git-lfs
• Everything else will be downloaded automatically when you build the docker image

Running the demo

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

docker-compose --file docker-compose_demo.yml up --build

If you The app wait 5 min for the db to initialize

Running your own system

Coming soon!

Folder moving

Optional

Purpose

To move files from an instrument computer to another location as soon as an analytical run is finished (e.g. a network drive). This way you don't need to run the whole QC system on the instrument computer. These scripts are written for Waters' raw folder and should not be used directly for anything else.

What the scripts are meant to do:

• Monitor when a run is done.
• Will check if the filename (really a folder name) has the expected number of delimiters.
• If the filename is in the right format the file will be move to the given location. This script was written for the metabolomics group at NEXS and there are therefore specific parsing of the filename to decide the destination folder.
  • The first string before the first delimiter is used as the project name and a project folder is create such that the file %infolder%\test-pro_pos_test-sample-metstd.raw will be moved to %outfolder%\test-pro.raw\Data\test-pro_pos_test-sample-metstd.raw
• Optionally symlinks can be made from the original location to the destination folder. This way you can still access the file as if it was still in the original place even if it is actually access in the destination location. So you can open the file normally in the instrument software that expect the file to exist at the original location.
• Optionally the above mentioned symlinks can be cleared my running a script.

Usage

• Copy the content of file_mover to the instrument computer where the files are located.

• Edit the top part of win_waters_mover.bat to point to the right folders and the settings you want.

  • infolder and outfolder are the source and destination folders respectively.
  • Like the QC system the file move expect to be able to parse information from the file name. So delim sets the character that separates the information.
  • expect_delims stats how many delimiters to expect in a filename. This is used to only parse files with the expected filename convention.
  • If symlinkback is TRUE a symbolic link will be made in the original location pointing to the destination location.

• If you use symlinks you need to:

  • Right click on Start → Run and launch "secpol.msc".
  • Open "Security Settings" → "Local Policies" → "User Rights Assignment" and select "Create symbolic links".
  • Click "Add User or Group..." → enter the username the system normally uses → click "Check Names" → Click "OK" → Click "OK"
  • Reboot or log out and log in again (or run "gpupdate/force" on the command-line as administrator).

• Edit monitor_folder.bat to point to the same input folder as in win_waters_mover.bat.

• Run enable_monitor_at_startup.bat. This should make the folder monitor start at reboot. A console windows will be visible if this worked (after reboot).

• If you used symlinks you can always remove all symlinks by running clear_symlink_folders.bat. Edit to set the location first. This should be same location as infolder in win_waters_mover.bat.

Troubleshooting

Get into the container. Can you ref container by name=???

docker exec -it b099a8f5f3c5  bash

RedHat

Install Docker on RedHat

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

git-lfs

sudo yum install docker git git-lfs

Other issues

Getting through firewall on linux

This might 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

Upgrade mariaDB

If you upgrade to a new version with an updated mariaDB version you might need to manuall update the database.

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.

docker exec -it qc4metabolomics-qc_process-1 bash

• qc4metabolomics-qc_shiny-1
• qc4metabolomics-qc_process-1
• qc4metabolomics-mariadb-1
• qc4metabolomics-ms_converter-1