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, 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

Versions

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, 

2.2.6-1,  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

• libgcc-ng >=10.3.0

• openjdk >=11

• python

Required By

• mosca

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"

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