recipe msp2db

Python package to create an SQLite database from a collection of MSP mass spectromertry spectra files. Currently works with MSP files formated as MassBank records or as MoNA records. The resulting SQLite database can be used for spectral matching with msPurity Bioconductor R package,

Homepage:

https://github.com/computational-metabolomics/msp2db

License:

GPL3 / GNU General Public v3 (GPLv3)

Recipe:

/msp2db/meta.yaml

package msp2db

(downloads) docker_msp2db

versions:

0.0.9-1,  0.0.9-0,  0.0.7-0,  0.0.6-0

depends pubchempy:

depends python:

depends six:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install msp2db

and update with::

   mamba update msp2db

To create a new environment, run:

mamba create --name myenvname msp2db

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/msp2db:<tag>

(see `msp2db/tags`_ for valid values for ``<tag>``)

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Link to this page

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