/MassBank-convert

Primary LanguageR

MassBank conversion

This container contains tools to convert MassBank SQL dumps into SQLite and mzVault formats. SQLite is convenient for use with RforMassSpectrometry Spectra/MsBackendMassbankSql, while mzVault is useful for use in Compound Discoverer.

Usage

  • Build the Docker container: docker build . -t massbank_convert

  • Download a MassBank SQL dump from https://github.com/MassBank/MassBank-data/releases/latest

  • If you are running your own MassBank instance with proprietary data: create an SQL dump using dump_massbank.sh on the MassBank host. This requires only Docker and Bash. Usage: ./dump_massbank.sh $INSTANCE [$TARGET], where $INSTANCE is the MassBank instance number (check docker ps if you don't know) and $TARGET is an optional path prefix (/tmp by default.) The script prints the path of the created dump, which is timestamped.

  • Convert the MassBank MariaDB dump to sqlite: docker run --rm -v /$DATADIR:/data massbank_convert /scripts/sqlite/gen_sqlite.sh $DUMPNAME.sql where $DATADIR is the directory in which the dump is stored and $DUMPNAME.sql is the filename. The converted database will be stored in the same directory with filename $DUMPNAME.db.

  • Convert the sqlite database to an mzVault database: docker run --rm -v /$DATADIR:/data massbank_convert /scripts/mzvault/gen_mzvault.sh $DUMPNAME.db where $DATADIR is the directory in which the dump is stored and $DUMPNAME.db is the filename. The converted database will be stored in the same directory with filename $DUMPNAME-mzvault.db.