cat-bro / gxtk

Command line utility for querying tool metadata on a Galaxy instance and performing various tasks

gxtk

Command line program querying the galaxy tool panel and performing miscellaneous tasks on galaxy instances. gxtk docs

Installation:

Installation within a virtual environment is recommended.

Install with pip

pip install git+https://github.com/cat-bro/gxtk.git

Alternative to installing with pip

Clone this repository. python gxtk.py in the root directory can be run in place of gxtk provided that the requirements are installed.

Galaxy authentication and configuration file

gxtk has command line options --galaxy_url (-g) and --api_key (-a) for logging into galaxy. Alternatively the command line option --profile (-p) can be used to select a profile from a configuration file with the path ~/.gxtk.yml. The location of the file can be overriden by setting the GXTK_PROFILES_PATH environment variable or using the --profiles_path command line option. gxtk uses the parsec style of configuration, with a yaml key for each profile and either url or url and key set for profile. The default profile key is set with the key __default. See example profiles file

To download the sample file

wget https://raw.githubusercontent.com/cat-bro/gxtk/main/.gxtk.yml.sample
mv .gxtk.yml.sample .gxtk.yml

gxtk find

Filter a list of installed tools on Galaxy based on repository name or tool display name. Results are returned as tab separated values. If an admin API key is supplied and the -e flag included, the result includes the name of the tool's conda environment.