recipe jmztab-m

This project is the reference reader, writer and validator implementation for mzTab for metabolomics 2.0+.

Homepage:

https://github.com/lifs-tools/jmztab-m

License:

APACHE / Apache License 2.0

Recipe:

/jmztab-m/meta.yaml

Links:

biotools: jmztab-m, doi: 10.5281/zenodo.3662402

mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches. This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information. mzTab-M has been developed with a view to support the following general tasks. Facilitate the sharing of final experimental results, especially with researchers outside the field of metabolomics. Export of results to external software, including programs such as Microsoft Excel and Open Office Spreadsheet and statistical software / coding languages such as R. Act as an output format of (web-) services that report MS-based results and thus can produce standardized result pages. Be able to link to the external experimental evidence e.g. by referencing back to mzML files.

package jmztab-m

(downloads) docker_jmztab-m

versions:

1.0.6-1,  1.0.6-0,  1.0.5-0,  1.0.4-0

depends openjdk:

>=11

depends python:

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 jmztab-m

and update with::

   mamba update jmztab-m

To create a new environment, run:

mamba create --name myenvname jmztab-m

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/jmztab-m:<tag>

(see `jmztab-m/tags`_ for valid values for ``<tag>``)

Notes

jmzTab-M is Java program that comes with a custom wrapper shell script. This shell wrapper is called "opsin" and is on $PATH by default. By default "-Xms512m -Xmx1g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "jmztab-m -Xms512m -Xmx1g"

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