recipe peptide-shaker

Independent platform for interpretation of proteomics identification results.

Homepage:

https://compomics.github.io/projects/peptide-shaker.html

Documentation:

https://github.com/compomics/peptide-shaker/blob/master/README.md

Developer docs:

https://github.com/compomics/peptide-shaker

License:

APACHE / Apache-2.0

Recipe:

/peptide-shaker/meta.yaml

Links:

biotools: peptide-shaker, usegalaxy-eu: peptide_shaker, doi: 10.1038/nbt.3109

PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, Metamorpheus, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!

package peptide-shaker

(downloads) docker_peptide-shaker

versions:
3.0.11-0,  3.0.8-0,  3.0.6-0,  3.0.4-0,  3.0.3-0,  3.0.1-0,  3.0.0-0,  2.2.25-0,  2.2.23-0, 

3.0.11-0,  3.0.8-0,  3.0.6-0,  3.0.4-0,  3.0.3-0,  3.0.1-0,  3.0.0-0,  2.2.25-0,  2.2.23-0,  2.2.17-0,  2.2.6-1,  2.2.6-0,  2.0.33-1,  2.0.33-0,  2.0.25-0,  2.0.18-1,  2.0.18-0,  2.0.15-1,  2.0.15-0,  2.0.14-0,  2.0.9-0,  2.0.5-0,  2.0.1.alpha-0,  1.16.40-1,  1.16.40-0,  1.16.36-0,  1.16.35-1,  1.16.35-0,  1.16.32-1,  1.16.31-1,  1.16.30-1,  1.16.29-1,  1.16.26-1,  1.16.23-0,  1.16.22-0,  1.16.20-0,  1.16.17-0,  1.16.16-2,  1.16.16-1,  1.16.16-0,  1.16.15-2,  1.16.15-1,  1.16.15-0,  1.16.14-0,  1.16.13-2,  1.16.13-1,  1.16.13-0,  1.16.4-2,  1.16.4-1,  1.16.4-0,  1.16.3-2,  1.16.3-1,  1.16.3-0,  1.16.0-2,  1.16.0-1,  1.16.0-0,  1.15.1-0,  1.15.0-0,  1.14.6-0,  1.14.4-0,  1.13.6-1,  1.13.6-0,  1.13.3-1,  1.13.3-0,  1.11.0-1,  1.11.0-0,  1.1.3-3,  1.1.3-2,  1.1.3-1

depends openjdk:

>=17

depends python:

requirements:

additional platforms:

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 peptide-shaker

and update with::

   mamba update peptide-shaker

To create a new environment, run:

mamba create --name myenvname peptide-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/peptide-shaker:<tag>

(see `peptide-shaker/tags`_ for valid values for ``<tag>``)

Notes

PeptideShaker 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 "peptide-shaker -Xms512m -Xmx1g"

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