We will just briefly cover the features available in gxadmin, there are lots of queries that may or may not be useful for your Galaxy instance and you will have to read the documentation before using them.

It started life as a small shell script that Helena wrote because she couldn’t remember what Gravity was called or where it could be found. Some of the functions needed for things like swapping zerglings are still included in gxadmin but are highly specific to UseGalaxy.eu and not generally useful.

Since then it became the home for “all of the SQL queries we [galaxy admins] run regularly.” @hexylena and @natefoo often shared SQL queries with each other in private chats, but this wasn’t helpful to the admin community at large, so they decided to put them all in gxadmin and make it as easy to install as possible. We are continually trying to make this tool more generic and generally useful, if you notice something that’s missing or broken, or have a new query you want to run, just let us know.

Agenda

1. Installing gxadmin
2. Configuration
3. Overview
4. Admin Favourite Queries
5. gxadmin for Monitoring
6. Implementing a Query
   1. A basic function
   2. Adding help
   3. Adding a query
7. Summary

Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

1. Step 1 ansible-galaxy
2. Step 2 tus
3. Step 3 cvmfs
4. Step 4 singularity
5. Step 5 tool-management
6. Step 6 data-library
7. Step 7 connect-to-compute-cluster
8. Step 8 job-destinations
9. Step 9 pulsar
10. Step 10 gxadmin
11. Step 11 monitoring
12. Step 12 tiaas
13. Step 13 reports
14. Step 14 ftp

Installing gxadmin

It’s simple to install gxadmin. Here’s how you do it, if you haven’t done it already.

Hands-on: Installing gxadmin with Ansible

1. Edit your requirements.yml and add the following:

   --- a/requirements.yml
   +++ b/requirements.yml
   @@ -28,3 +28,5 @@
      version: 0.1.0
    - src: galaxyproject.pulsar
      version: 1.0.8
   +- src: galaxyproject.gxadmin
   +  version: 0.0.8
      
   

   Tip: How to read a Diff

   If you haven’t worked with diffs before, this can be something quite new or different.

   If we have two files, let’s say a grocery list, in two files. We’ll call them ‘a’ and ‘b’.

   Old

   $ cat old
   🍎
   🍐
   🍊
   🍋
   🍒
   🥑
   

   New

   $ cat new
   🍎
   🍐
   🍊
   🍋
   🍍
   🥑
   

   We can see that they have some different entries. We’ve removed 🍒 because they’re awful, and replaced them with an 🍍

   Diff lets us compare these files

   $ diff old new
   5c5
   < 🍒
   ---
   > 🍍
   

   Here we see that 🍒 is only in a, and 🍍 is only in b. But otherwise the files are identical.

   There are a couple different formats to diffs, one is the ‘unified diff’

   $ diff -U2 old new
   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ new	2022-02-16 14:06:36.340962616 +0100
   @@ -3,4 +3,4 @@
    🍊
    🍋
   -🍒
   +🍍
    🥑
   

   This is basically what you see in the training materials which gives you a lot of context about the changes:

   • --- old is the ‘old’ file in our view
   • +++ new is the ‘new’ file
   • @@ these lines tell us where the change occurs and how many lines are added or removed.
   • Lines starting with a - are removed from our ‘new’ file
   • Lines with a + have been added.

   So when you go to apply these diffs to your files in the training:

   1. Ignore the header
   2. Remove lines starting with - from your file
   3. Add lines starting with + to your file

   The other lines (🍊/🍋 and 🥑) above just provide “context”, they help you know where a change belongs in a file, but should not be edited when you’re making the above change. Given the above diff, you would find a line with a 🍒, and replace it with a 🍍

   Added & Removed Lines

   Removals are very easy to spot, we just have removed lines

   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ new	2022-02-16 14:10:14.370722802 +0100
   @@ -4,3 +4,2 @@
    🍋
    🍒
   -🥑
   

   And additions likewise are very easy, just add a new line, between the other lines in your file.

   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ new	2022-02-16 14:11:11.422135393 +0100
   @@ -1,3 +1,4 @@
    🍎
   +🍍
    🍐
    🍊
   

   Completely new files

   Completely new files look a bit different, there the “old” file is /dev/null, the empty file in a Linux machine.

   $ diff -U2 /dev/null old
   --- /dev/null	2022-02-15 11:47:16.100000270 +0100
   +++ old	2022-02-16 14:06:19.697132568 +0100
   @@ -0,0 +1,6 @@
   +🍎
   +🍐
   +🍊
   +🍋
   +🍒
   +🥑
   

   And removed files are similar, except with the new file being /dev/null

   --- old	2022-02-16 14:06:19.697132568 +0100
   +++ /dev/null	2022-02-15 11:47:16.100000270 +0100
   @@ -1,6 +0,0 @@
   -🍎
   -🍐
   -🍊
   -🍋
   -🍒
   -🥑
   

2. Install the role with:

   Input: Bash

   ansible-galaxy install -p roles -r requirements.yml
   

3. Add the role to your playbook:

   --- a/galaxy.yml
   +++ b/galaxy.yml
   @@ -33,3 +33,4 @@
        - galaxyproject.nginx
        - galaxyproject.tusd
        - galaxyproject.cvmfs
   +    - galaxyproject.gxadmin
      
   

4. Run the playbook

   Input: Bash

   ansible-playbook galaxy.yml
   

With that, gxadmin should be installed! Now, test it out:

Hands-on: Test out gxadmin

1. Run gxadmin as the galaxy user and list recently registered users:

   Input: Bash

   sudo -u galaxy gxadmin query latest-users
   

   Input: Output

    id |          create_time          | disk_usage | username |       email        | groups | active
   ----+-------------------------------+------------+----------+--------------------+--------+--------
     1 | 2021-06-09 12:25:59.299651+00 | 218 kB     | admin    | admin@example.org  |        | f
   (1 rows)
   

1.sh

Configuration

If psql runs without any additional arguments, and permits you to access your galaxy database then you do not need to do any more configuration for gxadmin. Otherwise, you may need to set some of the PostgreSQL environment variables

Overview

gxadmin has several categories of commands, each with different focuses. This is not a technically meaningful separation, it is just done to make the interface easier for end users.

Admin Favourite Queries

@slugger70’s favourite: gxadmin query old-histories. He contributed this function to find old histories, as their instance has a 90 day limit on histories, anything older than that might be automatically removed. This helps their group identify any histories that can be purged in order to save space. Running this on UseGalaxy.eu, we have some truly ancient histories, and maybe could benefit from a similar policy.

@natefoo’s favourite: gxadmin query job-inputs. He contributed this function which helps him debug jobs which are not running and should be.

@bgruening’s favourite: gxadmin query latest-users let’s us see who has recently joined our server. We sometimes notice that people are running a training on our infrastructure and they haven’t registered for training infrastructure as a service which helps us coordinate infrastructure for them so they don’t have bad experiences.

@hexylena’s favourite gxadmin report job-info. This command gives more information than you probably need on the execution of a specific job, formatted as markdown for easy sharing with fellow administrators.

# Galaxy Job 5132146

Property      | Value
------------- | -----
         Tool | toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7
        State | running
      Handler | handler_main_2
      Created | 2019-04-20 11:04:40.854975+02 (3 days 05:49:30.451719 ago)
Job Runner/ID | condor / 568537
        Owner | e08d6c893f5

## Destination Parameters

Key                     |   Value
---                     |   ---
description             |   `canu`
priority                |   `-128`
request_cpus            |   `20`
request_memory          |   `64G`
requirements            |   `GalaxyGroup == "compute"`
tmp_dir                 |   `True`

## Dependencies

Name   |   Version   |   Dependency Type   |   Cacheable   |   Exact   |   Environment Path                          |   Model Class
---    |   ---       |   ---               |   ---         |   ---     |   ---                                       |   ---
canu   |   1.7       |   conda             |   false       |   true    |   /usr/local/tools/_conda/envs/__canu@1.7   |   MergedCondaDependency

## Tool Parameters

Name                 |   Settings
---------            |   ------------------------------------
minOverlapLength     |   500
chromInfo            |   /opt/galaxy/tool-data/shared/ucsc/chrom/?.len
stage                |   all
contigFilter         |   {lowCovDepth: 5, lowCovSpan: 0.5, minLength: 0, minReads: 2, singleReadSpan: 1.0}
s                    |   null
mode                 |   -nanopore-raw
dbkey                |   ?
genomeSize           |   300000
corOutCoverage       |   40
rawErrorRate         |
minReadLength        |   1000
correctedErrorRate   |

## Inputs

Job ID    |   Name                |   Extension     |   hda-id    |   hda-state   |   hda-deleted   |   hda-purged   |   ds-id     |   ds-state   |   ds-deleted   |   ds-purged   |   Size
----      |   ----                |   ----          |   ----      |   ----        |   ----          |   ----         |   ----      |   ----       |   ----         |   ----        |   ----
4975404   |   Osur_record.fastq   |   fastqsanger   |   9517188   |               |   t             |   f            |   9015329   |   ok         |   f            |   f           |   3272 MB
4975404   |   Osur_record.fastq   |   fastqsanger   |   9517188   |               |   t             |   f            |   9015329   |   ok         |   f            |   f           |   3272 MB

## Outputs

Name                                          |   Extension   |   hda-id    |   hda-state   |   hda-deleted   |   hda-purged   |   ds-id     |   ds-state   |   ds-deleted   |   ds-purged   |   Size
----                                          |   ----        |   ----      |   ----        |   ----          |   ----         |   ----      |   ----       |   ----         |   ----        |   ----
Canu assembler on data 41 (trimmed reads)     |   fasta.gz    |   9520369   |               |   f             |   f            |   9018510   |   running    |   f            |   f           |
Canu assembler on data 41 (corrected reads)   |   fasta.gz    |   9520368   |               |   f             |   f            |   9018509   |   running    |   f            |   f           |
Canu assembler on data 41 (unitigs)           |   fasta       |   9520367   |               |   f             |   f            |   9018508   |   running    |   f            |   f           |
Canu assembler on data 41 (unassembled)       |   fasta       |   9520366   |               |   f             |   f            |   9018507   |   running    |   f            |   f           |
Canu assembler on data 41 (contigs)           |   fasta       |   9520365   |               |   f             |   f            |   9018506   |   running    |   f            |   f           |

gxadmin for Monitoring

gxadmin already supported query, csvquery, and tsvquery for requesting data from the Galaxy database in tables, CSV, or TSV formats, but we recently implemented influx queries which output data in a format that Telegraf can consume.

So running gxadmin query queue-overview normally shows something like:

The gxadmin iquery queue-overview is run by our Telegraf monitor on a regular basis, allowing us to consume the data:

queue-overview,tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0,tool_version=0.4.6.0,state=running,handler=handler_main_4,destination_id=12cores_180G_special,job_runner_name=condor count=1
queue-overview,tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0,tool_version=0.4.6.0,state=running,handler=handler_main_5,destination_id=12cores_180G_special,job_runner_name=condor count=1
queue-overview,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0,tool_version=1.1.0.46-0,state=running,handler=handler_main_3,destination_id=12cores_12G,job_runner_name=condor count=1
queue-overview,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1,tool_version=1.0.0_rc1+galaxy1,state=queued,handler=handler_main_11,destination_id=4G_memory,job_runner_name=condor count=1
queue-overview,tool_id=toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3,tool_version=2.1.0+galaxy3,state=running,handler=handler_main_11,destination_id=8cores_20G,job_runner_name=condor count=1
queue-overview,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72,tool_version=0.72,state=running,handler=handler_main_11,destination_id=20G_memory,job_runner_name=condor count=4
queue-overview,tool_id=ebi_sra_main,tool_version=1.0.1,state=running,handler=handler_main_3,destination_id=4G_memory,job_runner_name=condor count=2
queue-overview,tool_id=ebi_sra_main,tool_version=1.0.1,state=running,handler=handler_main_4,destination_id=4G_memory,job_runner_name=condor count=3

And produce some nice graphs from it.

You can use an influx configuration like:

[[inputs.exec]]
    commands = ["/usr/bin/galaxy-queue-size"]
    timeout = "10s"
    data_format = "influx"
    interval = "1m"

This often requires a wrapper script, because you’ll need to pass environment variables to the gxadmin invocation, e.g.:

#!/bin/bash
export PGUSER=galaxy
export PGHOST=dbhost
gxadmin iquery queue-overview --short-tool-id
gxadmin iquery workflow-invocation-status

Tip: Which queries support iquery?

This data is not currently exposed, so, just try the queries. But it’s easy to add influx support when missing! Here is an example, we set the variables in a function:

fields="count=1"
tags="tool_id=0"

This means: column 0 is a tag named tool_id, and column 1 is a field (real value) named count. Here is an example that has multiple fields that are stored.

Implementing a Query

Queries are really easy to implement! All you have to do is add your SQL, with a small bash function to wrap it. gxadmin supports ‘local’ functions, which you can add locally without contributing back. We strongly encourage you to contribute your functions back to gxadmin though, you’ll never know who wants to know the same thing about their db.

gxadmin will look for local functions in ~/.config/gxadmin-local.sh

A basic function

Hands-on: Implementing a basic function

1. If ~/.config/ does not exist, create that directory with mkdir -p ~/.config/

2. Open ~/.config/gxadmin-local.sh in a text editor.

3. Add the following to the file and save it.

   local_hello() { ## : Says hi
   	echo "hi!"
   }
   

4. Run gxadmin local

   Question

   What do you see?

   Solution

   It should look like:

   gxadmin usage:
   
   Local: (These can be configured in /home/hxr/.config/gxadmin-local.sh)
   
       local hello          Says hi
   
   help / -h / --help : this message. Invoke '--help' on any subcommand for help specific to that subcommand
   

5. Run gxadmin local hello

   Question

   What do you see?

   Solution

   It should output ‘hi!’

This is the simplest possible function you can add, and is pretty limited in its functionality. This can offer you a nice place to put all of your existing bash scripts, and have autogenerated help for them.

Adding help

Every function is improved by documentation! Let’s add that now:

Hands-on: Adding help

1. Open ~/.config/gxadmin-local.sh in a text editor.

2. Update your function to add the handle_help call:

   local_hello() { ## : Says hi
   	handle_help "$@" <<-EOF
   		Greets you
   	EOF
   	echo "hi!"
   }
   

3. Run gxadmin local hello --help

   Question

   What do you see?

   Solution

   It should look like:

   $ gxadmin local hello --help
   **NAME**
   
   local hello - Says hi
   
   **SYNOPSIS**
   
   gxadmin local hello
   
   **NOTES**
   
   Greets you
   

Adding a query

The bulk of gxadmin is not functions calling shell commands though, it’s mostly SQL queries. So let’s find the N most recent jobs

Hands-on: Adding a query

1. Open ~/.config/gxadmin-local.sh in a text editor.

2. Add a new function:

   local_query-latest() { ## [jobs|10]: Queries latest N jobs (default to 10)
   	handle_help "$@" <<-EOF
   		Find information about the latest jobs on your server.
   	EOF
   
   	# Value of first argument, or 10 if isn't supplied
   	job_limit=${1:-10}
   
   	# Here we store the query in a bash variable named QUERY
   	read -r -d '' QUERY <<-EOF
   		SELECT
   			id, tool_id, tool_version, state
   		FROM job
   		ORDER BY id desc
   		LIMIT ${job_limit}
   	EOF
   }
   

3. Run gxadmin local query-latest 5 to select

   Question

   What do you see?

   Solution

   It should similar to the following, assuming you’ve run tools in your Galaxy

   $ gxadmin local query-latest 5
    id  |         tool_id          | tool_version | state
   -----+--------------------------+--------------+-------
    103 | upload1                  | 1.1.6        | ok
    102 | upload1                  | 1.1.6        | ok
    101 | upload1                  | 1.1.6        | error
    100 | circos                   | 0.91         | ok
     99 | circos                   | 0.91         | ok
   (5 rows)
   

Summary

There are a lot of queries, all tailored to specific use cases, some of these may be interesting for you, some may not. These are all documented with example inputs and outputs in the gxadmin readme, and help is likewise available from the command line.

Comment: Got lost along the way?

If you missed any steps, you can compare against the reference files, or see what changed since the previous tutorial.

If you’re using git to track your progress, remember to add your changes and commit with a good commit message!

Key points

• gxadmin is a tool to run common database queries useful for Galaxy admins

• new queries are welcome and easy to contribute

Frequently Asked Questions

Feedback

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Citing this Tutorial

1. Helena Rasche, Galaxy Monitoring with gxadmin (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html Online; accessed TODAY
2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{admin-gxadmin,
author = "Helena Rasche",
title = "Galaxy Monitoring with gxadmin (Galaxy Training Materials)",
year = "",
month = "",
day = ""
url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html}",
note = "[Online; accessed TODAY]"
}
@article{Batut_2018,
    doi = {10.1016/j.cels.2018.05.012},
    url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
    year = 2018,
    month = {jun},
    publisher = {Elsevier {BV}},
    volume = {6},
    number = {6},
    pages = {752--758.e1},
    author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
    title = {Community-Driven Data Analysis Training for Biology},
    journal = {Cell Systems}
}