Galaxy Monitoring with gxadmin

Authors: orcid logoHelena Rasche avatar Helena Rasche
Overview
Creative Commons License: CC-BY Questions:
  • What is gxadmin

  • What can it do?

  • How to write a query?

Objectives:
  • Learn gxadmin basics

  • See some queries and learn how they help debug production issues

Time estimation: 30 minutes
Supporting Materials:
Published: Jan 28, 2019
Last modification: Feb 1, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00009
rating Rating: 4.7 (0 recent ratings, 3 all time)
version Revision: 27

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.” Helena Rasche avatar Helena Rasche and Nate Coraor avatar Nate Coraor 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. 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
    backup-cleanup
  3. Step 3
    customization
  4. Step 4
    tus
  5. Step 5
    cvmfs
  6. Step 6
    apptainer
  7. Step 7
    tool-management
  8. Step 8
    reference-genomes
  9. Step 9
    data-library
  10. Step 10
    dev/bioblend-api
  11. Step 11
    connect-to-compute-cluster
  12. Step 12
    job-destinations
  13. Step 13
    pulsar
  14. Step 14
    celery
  15. Step 15
    gxadmin
  16. Step 16
    reports
  17. Step 17
    monitoring
  18. Step 18
    tiaas
  19. Step 19
    sentry
  20. Step 20
    ftp
  21. Step 21
    beacon

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: 6.1.0
     - name: usegalaxy_eu.rabbitmqserver
       version: 1.4.1
    +- src: galaxyproject.gxadmin
    +  version: 0.0.12
       
    

    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’.

    Input: Old
    $ cat old
    🍎
    🍐
    🍊
    🍋
    🍒
    🥑
    Output: 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
    @@ -34,3 +34,4 @@
         - 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)
    

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.

Category Keyword Purpose
Configuration config Commands relating to galaxy’s configuration files like XML validation.
Filters filter Transforming streams of text.
Galaxy Admin galaxy Miscellaneous galaxy related commands like a cleanup wrapper.
uWSGI uwsgi If you’re using systemd for Galaxy and a handler/zergling setup, then this lets you manage your handlers and zerglings.
DB Queries {csv,tsv,i,}query Queries against the database which return tabular output.
Report report Queries which return more complex and structured markdown reports.
Mutations mutate These are like queries, except they mutate the database. All other queries are read-only.
Meta meta More miscellaneous commands, and a built-in updating function.

Admin Favourite Queries

Simon Gladman avatar Simon Gladman ‘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.

Input
gxadmin query old-histories
Output
id update-time user-id email name published deleted purged hid-counter
361 2013-02-24 16:27:29.197572 xxx xxxx Unnamed history f f f 6
362 2013-02-24 15:31:05.804747 xxx xxxx Unnamed history f f f 1
347 2013-02-22 15:59:12.044169 xxx xxxx Unnamed history f f f 19
324 2013-02-22 15:57:54.500637 xxx xxxx Exercise 5 f f f 64
315 2013-02-22 15:50:51.398894 xxx xxxx day5 practical f f f 90
314 2013-02-22 15:45:47.75967 xxx xxxx 5. Tag Galaxy-Kurs f f f 78

Nate Coraor avatar Nate Coraor ‘s favourite: gxadmin query job-inputs. He contributed this function which helps him debug jobs which are not running and should be.

Input
gxadmin query job-inputs 5 # Or another job ID
hda-id hda-state hda-deleted hda-purged d-id d-state d-deleted d-purged object-store-id
8638197   f f 8246854 running f f files9
8638195   f f 8246852 running f f files9
8638195   f f 8246852 running f f files9

Björn Grüning avatar Björn Grüning ‘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.

Input
gxadmin query latest-users
id create_time disk_usage username email groups active
3937 2019-01-27 14:11:12.636399 291 MB xxxx xxxx   t
3936 2019-01-27 10:41:07.76126 1416 MB xxxx xxxx   t
3935 2019-01-27 10:13:01.499094 2072 kB xxxx xxxx   t
3934 2019-01-27 10:06:40.973938 0 bytes xxxx xxxx   f
3933 2019-01-27 10:01:22.562782   xxxx xxxx   f

Helena Rasche avatar Helena Rasche ‘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.

Input
gxadmin report job-info 1
Output
# 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           |

Catherine Bromhead avatar Catherine Bromhead contributed the ‘jobs’ query: gxadmin query jobs lets you list jobs that have been run on your Galaxy. It’s a lot more flexible than queue-overview and we suggest using it instead, in most places. E.g. to find circos jobs that were recently run:

Input
gxadmin query jobs --limit 2  --tool circos
job_id create_time update_time user_id state tool_id handler destination external_id
58483488 2023-04-04 18:42:40 2023-04-04 18:43:30   error toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy8 handler_sn06_5 1cores_10.0G 42071736
58483208 2023-04-04 18:36:24 2023-04-04 18:40:43   error toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9 handler_sn06_3 1cores_10.0G 42071486

or to see recent jobs from a specific user (e.g. to help answer their email queries when they just send you a screenshot rather than a proper bug report)

Input
gxadmin query jobs --limit 2 --user helena-rasche --terminal
job_id create_time update_time user_id state tool_id handler destination external_id
58277473 2023-03-31 09:53:36 2023-03-31 09:53:36 580 ok TAG_FROM_FILE default    
58277410 2023-03-31 09:47:16 2023-03-31 09:51:26 580 ok toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 handler_sn06_0 1cores_4.0G 41859564

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:

Input
gxadmin query queue-overview
tool_id tool_version destination_id handler state job_runner_name count
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0 0.4.6.0 12cores_180G_special handler_main_4 running condor 1
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0 0.4.6.0 12cores_180G_special handler_main_5 running condor 1
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0 1.1.0.46-0 12cores_12G handler_main_3 running condor 2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_extract_barcodes/qiime_extract_barcodes/1.9.1.0 1.9.1.0 4G_memory handler_main_1 running condor 1
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3 2.1.0+galaxy3 8cores_20G handler_main_11 running condor 1
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 0.72 20G_memory handler_main_11 running condor 4
ebi_sra_main 1.0.1 4G_memory handler_main_3 running condor 2
ebi_sra_main 1.0.1 4G_memory handler_main_4 running condor 3

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

Input
gxadmin iquery queue-overview
Output
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

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.

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.

Hands-on: Time to git commit

It’s time to commit your work! Check the status with

git status

Add your changed files with

git add ... # any files you see that are changed

And then commit it!

git commit -m 'Finished Galaxy Monitoring with gxadmin'

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!

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
    backup-cleanup
  3. Step 3
    customization
  4. Step 4
    tus
  5. Step 5
    cvmfs
  6. Step 6
    apptainer
  7. Step 7
    tool-management
  8. Step 8
    reference-genomes
  9. Step 9
    data-library
  10. Step 10
    dev/bioblend-api
  11. Step 11
    connect-to-compute-cluster
  12. Step 12
    job-destinations
  13. Step 13
    pulsar
  14. Step 14
    celery
  15. Step 15
    gxadmin
  16. Step 16
    reports
  17. Step 17
    monitoring
  18. Step 18
    tiaas
  19. Step 19
    sentry
  20. Step 20
    ftp
  21. Step 21
    beacon