Galaxy Admin Utility

A command line tool for Galaxy administrators to run common queries against our Postgres databases. It additionally includes some code for managing zerglings under systemd, and other utilities.

Mostly gxadmin acts as a repository for the common queries we all run regularly but fail to share with each other. We even include some unlisted queries which may be useful as examples, but are not generically useful.

It comes with around 90 commonly useful queries included (180+ commands total), but you can easily add more to your installation with local functions. gxadmin attempts to be a very readable bash script and avoids using fancy new bash features.

Subcommand	Functions
query	89
server	22
mutate	16
meta	12
uwsgi	11
galaxy	11
report	3
filter	3
config	2
cluster	1

This script strictly expects a postgres database and has no plans to support mysql or sqlite3.

Installation

curl -L https://github.com/galaxyproject/gxadmin/releases/latest/download/gxadmin > /usr/bin/gxadmin
chmod +x /usr/bin/gxadmin

Contributing

See CONTRIBUTING.md

Changelog

Contributors

Helena Rasche, BDFL (@hexylena)
Nate Coraor (@natefoo)
Simon Gladman (@slugger70)
Anthony Bretaudeau (@abretaud)
John Chilton (@jmchilton)
Gianmauro Cuccuru (@gmauro)
Lucille Delisle (@lldelisle)
Manuel Messner (mm@skellet.io)
Kim Brügger (@bruggerk)

License

GPLv3

Configuration

gxadmin does not have much configuration, mostly env vars and functions will complain if you don't have them set properly.

Postgres

Queries support being run in normal postgres table, csv, or tsv output as you need. Just use gxadmin query, gxadmin tsvquery, or gxadmin csvquery as appropriate.

You should have a ~/.pgpass with the database connection information, and set PGDATABASE, PGHOST, and PGUSER in your environment.

Example .pgpass:

<pg_host>:5432:*:<pg_user>:<pg_password>

InfluxDB

In order to use functions like gxadmin meta influx-post, gxadmin requires a few environment variables to be set. Namely

INFLUX_URL
INFLUX_PASS
INFLUX_USER
INFLUX_DB

GDPR

You may want to set GDPR_MODE=1. Please determine your own legal responsibilities, the authors take no responsibility for anything you may have done wrong.

If you want to publish data, first be careful! Second, the GDPR_MODE variable is part of the hash, so you can set it to something like GDPR_MODE=$(openssl rand -hex 24 2>/dev/null) gxadmin query ... for hashing and "throwing away the key"

Local Functions

If you want to add some site-specific functions, you can do this in ~/.config/gxadmin-local.sh (location can be overridden by setting $GXADMIN_SITE_SPECIFIC)

You should write a bash script which looks like. ALL functions must be prefixed with local_

local_cats() { ## : Makes cat noises
	handle_help "$@" <<-EOF
		Here is some documentation on this function
	EOF

	echo "Meow"
}

This can then be called with gxadmin like:

$ gxadmin local cats --help
gxadmin local functions usage:

    cats   Cute kitties

help / -h / --help : this message. Invoke '--help' on any subcommand for help specific to that subcommand
$ gxadmin local cats
Meow
$

If you prefix the function name with query-, e.g. local_query-cats, then it will be run as a database query. CSV/TSV/Influx queries are not currently supported.

gmauro/gxadmin