Usage

1. Downloading Massbank

svn checkout http://www.massbank.jp/SVN/OpenData/record/

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

3. use python script to generate mzML

python parseMBFiles.py allMBFiles/

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