Usage

0. Get dependencies

pip install numpy
pip install pyopenms

1. Downloading Massbank

git clone https://github.com/MassBank/MassBank-data.git

2. Copying all the individual Massbank records into allMBFiles folder

For windows :
http://stackoverflow.com/questions/585091/using-xcopy-to-copy-files-from-several-directories-to-one-directory

For Mac/Unix :
http://unix.stackexchange.com/questions/67503/move-all-files-with-a-certain-extension-from-multiple-subdirectories-into-one-di

Or: find /path/to/MassBank-data/ -name "*.txt" | xargs -I % ln -s % allMBFiles

3. use python script to generate mzML

python parseMBFiles.py allMBFiles/

As docker conversion from https://github.com/MassBank/MassBank-data all-in-one. From within the checked-out working copy of MassBankUpdate:

docker run --rm -v $PWD:/MBU hroest/openms-pyopenms-v2.2.0 /MBU/convert-massbank.sh'

Note : For updating MB2HMDBmapping.csv you need to update HMDB first : https://github.com/epoyraz/updateHMDB