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https://github.com/galaxyproject/gxadmin
Handy command line utility for Galaxy administrators :rocket:
https://github.com/galaxyproject/gxadmin
automation galaxy galaxy-project hacktoberfest postgres-databases sql sysadmin
Last synced: about 1 month ago
JSON representation
Handy command line utility for Galaxy administrators :rocket:
- Host: GitHub
- URL: https://github.com/galaxyproject/gxadmin
- Owner: galaxyproject
- License: gpl-3.0
- Created: 2018-10-05T15:45:51.000Z (almost 6 years ago)
- Default Branch: main
- Last Pushed: 2024-04-05T01:30:41.000Z (3 months ago)
- Last Synced: 2024-04-11T16:03:10.983Z (3 months ago)
- Topics: automation, galaxy, galaxy-project, hacktoberfest, postgres-databases, sql, sysadmin
- Language: Shell
- Homepage: https://galaxyproject.github.io/gxadmin/#/
- Size: 1.75 MB
- Stars: 22
- Watchers: 20
- Forks: 26
- Open Issues: 16
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Lists
- awesome-galaxy - gxadmin - shell tools
README
# gxadmin: Make Galaxy administration magical 🌈
A command line tool for [Galaxy](https://github.com/galaxyproject/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.
## Installation
```
curl -L https://github.com/galaxyproject/gxadmin/releases/latest/download/gxadmin > /usr/bin/gxadmin
chmod +x /usr/bin/gxadmin
```
## Contributing
See [CONTRIBUTING.md](./CONTRIBUTING.md)
## Changelog
[Changelog](CHANGELOG.md)
## Contributors
- Helena Rasche, BDFL ([@hexylena](https://github.com/hexylena)) 🏳️🌈🏳️⚧️
- Nate Coraor ([@natefoo](https://github.com/natefoo))
- Simon Gladman ([@slugger70](https://github.com/slugger70))
- Anthony Bretaudeau ([@abretaud](https://github.com/abretaud))
- John Chilton ([@jmchilton](https://github.com/jmchilton))
- Gianmauro Cuccuru ([@gmauro](https://github.com/gmauro))
- Lucille Delisle ([@lldelisle](https://github.com/lldelisle))
- Manuel Messner ([email protected])
- Kim Brügger ([@bruggerk](https://github.com/bruggerk))
- Catherine Bromhead ([@cat-bro](https://github.com/cat-bro))
- Michelle Savage ([@hujambo-dunia](https://github.com/hujambo-dunia))
## 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:
```
:5432:*::
```
### 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`
### Other Environment Variables
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/`
### 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_`**
```bash
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:
```console
$ 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.