Mercurial > repos > galaxyp > mz_to_sqlite

view README.md @ 6:f52c286f7e0b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 24561502a9bed97f351af6a0438aa82414a351ab"
author galaxyp
date Sat, 30 Oct 2021 13:05:57 +0000
parents 9a1ced29b130
children
line wrap: on
line source

# MzToSQLite

## Description

Parses MzIdentML, FASTA and MGF scan files into a SQLite3 database. The schema is used by MVPApplication in visualizing the parsed data.

## General Requirements

MzToSQLite is threaded during the read stages of processing. It is single threaded during SQL writes. It will perform best when given one core per MGF file. But it runs well with between two and four cores.

Reading the MGF files is memory intensive, set the _JAVA_OPTIONS to the minimum recommended below.

**Example Recommended Settings**

    One core, minimum memory:
        _JAVA_OPTIONS: -Xms20G -Xmx20G

    Four core, slightly faster performance (performance determined by size of each MGF file):
        _JAVA_OPTIONS: -Xms40G -Xmx40G