recipe kinamine_y_shaker

Kinamine is a tool to export all phospho-peptides that were discovered by a mass spec search program

Homepage:

https://github.com/LaurieParkerLab/KinamineY-shaker

License:

APACHE / Apache License 2.0

Recipe:

/kinamine_y_shaker/meta.yaml

Links:

doi: 10.1021/ja507164a

Kinamine searches for phosphopeptides that were discovered by a mass spec search program (in this case Peptide Shaker) and outputs those peptides into a single file. The peptides are centered on their phosphorylated amino acid.

package kinamine_y_shaker

versions:

1.0.0-1,  1.0.0-0

depends openjdk:

>=8

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 kinamine_y_shaker

and update with::

   mamba update kinamine_y_shaker

To create a new environment, run:

mamba create --name myenvname kinamine_y_shaker

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/kinamine_y_shaker:<tag>

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

Notes

Kinamine is a Java program originally written by Kevin Murray of UMN and updated by John Blankenhorn also of UMN

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