recipe dia_umpire

DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.

Homepage:

https://github.com/Nesvilab/DIA-Umpire

License:

Apache License, Version 2.0

Recipe:

/dia_umpire/meta.yaml

Links:

doi: 10.1038/nmeth.3255

package dia_umpire

(downloads) docker_dia_umpire

versions:

2.1.6-1,  2.1.6-0,  2.1.3-1,  2.1.3-0,  2.1.2-0

depends openjdk:

>=7

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 dia_umpire

and update with::

   mamba update dia_umpire

To create a new environment, run:

mamba create --name myenvname dia_umpire

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/dia_umpire:<tag>

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

Notes

DIA-Umpire is a Java program.

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Link to this page

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