Docker Installation
1. Pulling the docker image:
docker pull docker pull lincoln1010/mass_spectrometry_file_converter:v2.1.1
2. 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
info
Default value set for CPU is 1 and THREAD is 1
3. Enabling the docker in docker (which is necessary):
docker exec < name of the container > dockerd >/tmp/docker.stdout 2>/tmp/docker.stderr &
tip
The converter supports all arguments listed on the MSConvert website.
Step 4 describes on how to add there arguments/parameters.
4. Copy extra parameters on config.txt file:
- a : create a config.txt file with content , for example, --mzXML (without any indentation)
- b :
docker cp < path to your config.txt file > < name of the container >:/app/config.txt(copying the config.txt file to /app/config.txt inside the container)