MS File Converter CWL-Based
Installation
Mass Spectometry File Coverter.
Requirements
The following packages are essential for the proper functioning of the converter service
Ways of using the converter
The converter servie can be installed or deployed in three different ways:
This is for installlation of items on local machine
Clone the repository
git clone https://github.com/NFDI4Chem/cs-ms-converter.git
Go inside the folder msconverter-cwl-based
cd msconverter-cwl-based
Create a python virtual environment and activate it
How to create a python virtual environment
python3 -m venv <your desired virtual environment name>
Activate the environment
source <path to your desired virtual environment name>/bin/activate
Install necessary requirements
pip install -r requirements.txt
Run the main file rest_api.py
rest_api.py
python rest_api.py
or
rest_api.py
python rest_api.py
URL will be available on http://localhost:5000/api-docs#
This is for installlation of items on Docker
Pull the Docker Image
docker pull docker pull lincoln1010/mass_spectrometry_file_converter:v2.1.1
Running the container:
docker run --privileged -d -ti --name < name of the container > -p 5000:5000 -e CPU=<number of cpu eg: 1> -e THREAD=<number of threads eg: 1> lincoln1010/mass_spectrometry_file_converter:v2.1.1
Enabling the docker in docker (which is necessary):
docker exec < name of the container > dockerd >/tmp/docker.stdout 2>/tmp/docker.stderr &
The converter supports all arguments listed on the MSConvert Documentation.
Copy extra parameters on config.txt file:
- Create a config.txt file with content , for example, --mzXML (without any indentation)
- Copying config.txt file to /app/config.txt inside the container
docker cp < path to your config.txt file > < name of the container >:/app/config.txt
URL will be available on http://localhost:5000/api-docs#
The deployment of Kubernetes instance is done via Helm chart. The helmchart repository is available at Helm Chart: Mass Sptrometry File Converter
Clone the repository
git clone https://git.rwth-aachen.de/linsherpa/msconverter-helmchart.git
Provide necessary changes on the values.yaml such as name of app, namespace, persistent volume claims, APIConnection timeouts, CPU , THREAD, etc
Command for deploying Helm Chart
helm install -f values.yaml < name-of-the-helm-app > .