recipe peptide-shaker

Independent platform for interpretation of proteomics identification results

Homepage

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

License

APACHE / Apache License 2.0

Recipe

/peptide-shaker/meta.yaml

Links

biotools: 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+, 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
2.0.1.alpha-01.16.40-11.16.40-01.16.36-01.16.35-11.16.35-01.16.32-11.16.31-11.16.30-1

2.0.1.alpha-01.16.40-11.16.40-01.16.36-01.16.35-11.16.35-01.16.32-11.16.31-11.16.30-11.16.29-11.16.26-11.16.23-01.16.22-01.16.20-01.16.17-01.16.16-11.16.16-01.16.15-11.16.15-01.16.14-01.16.13-11.16.13-01.16.4-11.16.4-01.16.3-11.16.3-01.16.0-11.16.0-01.15.1-01.15.0-01.14.6-01.14.4-01.13.6-11.13.6-01.13.3-11.13.3-01.11.0-11.11.0-01.1.3-31.1.3-21.1.3-1

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install peptide-shaker

and update with:

conda update peptide-shaker

or 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"