recipe searchgui

User-friendly graphical tool for using proteomics identification search engines

Homepage

https://github.com/compomics/searchgui

License

APACHE / Apache License 2.0

Recipe

/searchgui/meta.yaml

Links

biotools: searchgui, doi: 10.1002/pmic.201000595

SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA.

package searchgui

(downloads) docker_searchgui

Versions
4.0.1.alpha-03.3.10-03.3.9-13.3.9-03.3.6-13.3.5-13.3.3-13.3.1-13.3.1-0

4.0.1.alpha-03.3.10-03.3.9-13.3.9-03.3.6-13.3.5-13.3.3-13.3.1-13.3.1-03.2.26-03.2.24-03.2.20-03.2.13-13.2.13-03.2.11-13.2.11-03.2.8-13.2.8-03.2.7-13.2.7-03.2.6-13.2.6-03.2.5-13.2.5-03.2.3-13.2.3-03.1.4-23.1.4-13.1.4-02.9.0-22.9.0-12.9.0-02.1.4-32.1.4-22.1.4-12.1.4-0

Depends
Required By

Installation

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

conda install searchgui

and update with:

conda update searchgui

or use the docker container:

docker pull quay.io/biocontainers/searchgui:<tag>

(see searchgui/tags for valid values for <tag>)

Notes

SearchGUI 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 "searchgui -Xms512m -Xmx1g"