- recipe kinamine_y_shaker
Kinamine is a tool to export all phospho-peptides that were discovered by a mass spec search program
- Homepage:
- License:
APACHE / Apache License 2.0
- Recipe:
- 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:
on openjdk
>=8on 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 kinamine_y_shaker
to add into an existing workspace instead, run:
pixi add kinamine_y_shaker
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 kinamine_y_shaker
Alternatively, to install into a new environment, run:
conda create -n envname kinamine_y_shaker
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/kinamine_y_shaker:<tag>
(see kinamine_y_shaker/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¶
Kinamine is a Java program originally written by Kevin Murray of UMN and updated by John Blankenhorn also of UMN
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/kinamine_y_shaker/README.html)
