Command line program querying the galaxy tool panel and performing miscellaneous tasks on galaxy instances. gxtk docs
Installation within a virtual environment is recommended.
pip install git+https://github.com/cat-bro/gxtk.git
Clone this repository. python gxtk.py in the root directory can be run in place of gxtk provided that the requirements are installed.
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
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.