A command line tool for Galaxy administrators to run common queries against our Postgres databases. It additionally includes some code for managing Galaxy and associated features, and other utilities.
Mostly gxadmin acts as a repository for the common queries we all run regularly but fail to share with each other.
It comes with a wide array of useful queries that you might want to run, but you can also 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 | 104 |
| server | 22 |
| mutate | 22 |
| meta | 12 |
| galaxy | 12 |
| report | 5 |
| filter | 3 |
| config | 2 |
| cluster | 1 |
This script requires a postgres database and has no plans to support mysql or sqlite3.
If we do support sqlite3 in the future, it will be on a "if you're lucky" type basis, we won't be modifying queries to remove postgres-ism.
curl -L https://github.com/galaxyproject/gxadmin/releases/latest/download/gxadmin > /usr/bin/gxadmin
chmod +x /usr/bin/gxadmin
See CONTRIBUTING.md
- 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)
- Catherine Bromhead (@cat-bro)
- Michelle Savage (@hujambo-dunia)
GPLv3
gxadmin does not have much configuration, mostly env vars and functions will complain if you don't have them set properly.
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>
In order to use functions like gxadmin meta influx-post, gxadmin requires
a few environment variables to be set. Namely
INFLUX_URLINFLUX_PASSINFLUX_USERINFLUX_DB
Some subcommands may ask you to set these environment variables, if they aren't already.
| Variable | Example Value |
|---|---|
GALAXY_CONFIG_DIR |
/srv/galaxy/config/ |
GALAXY_CONFIG_FILE |
/srv/galaxy/config/galaxy.yml |
GALAXY_LOG_DIR |
/var/log/galaxy/ |
GALAXY_MUTABLE_CONFIG_DIR |
/srv/galaxy/var/ |
GALAXY_ROOT |
/srv/galaxy/server/ |
VIRTUAL_ENV |
/srv/galaxy/venv/ |
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"
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.