- recipe jmztab-m
This project is the reference reader, writer and validator implementation for mzTab for metabolomics 2.0+.
- Homepage:
- License:
APACHE / Apache License 2.0
- Recipe:
- 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¶
- Versions:
1.0.6-1,1.0.6-0,1.0.5-0,1.0.4-0- Depends:
on openjdk
>=11on python
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install jmztab-m
to add into an existing workspace instead, run:
pixi add jmztab-m
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install jmztab-m
Alternatively, to install into a new environment, run:
conda create -n envname jmztab-m
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/jmztab-m:<tag>
(see jmztab-m/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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"
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/jmztab-m/README.html)
