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-0, 3.3.10-0, 3.3.9-1, 3.3.9-0, 3.3.6-1, 3.3.5-1, 3.3.3-1, 3.3.1-1, 3.3.1-0, 3.2.26-0, 3.2.24-0, 3.2.20-0, 3.2.13-1, 3.2.13-0, 3.2.11-1, 3.2.11-0, 3.2.8-1, 3.2.8-0, 3.2.7-1, 3.2.7-0, 3.2.6-1, 3.2.6-0, 3.2.5-1, 3.2.5-0, 3.2.3-1, 3.2.3-0, 3.1.4-2, 3.1.4-1, 3.1.4-0, 2.9.0-2, 2.9.0-1, 2.9.0-0, 2.1.4-3, 2.1.4-2, 2.1.4-1, 2.1.4-0

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”