Authors: Helena Rasche
Overview
Questions:

• What can it do?

• How to write a query?

Objectives:

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

Time estimation: 30 minutes
Supporting Materials:
Last modification: Mar 27, 2023

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

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.

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

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
+  version: 0.0.8



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 new5c5< 🍒---> 🍍 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:

2. Remove lines starting with - from 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 🍍

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

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
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?

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

Have questions about this tutorial? Check out the tutorial FAQ page or the FAQ page for the Galaxy Server administration topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help Forum

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Citing this Tutorial

2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012



@misc{admin-gxadmin,
author = "Helena Rasche",
title = "Galaxy Monitoring with gxadmin (Galaxy Training Materials)",
year = "",
month = "",
day = ""
note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
doi = {10.1371/journal.pcbi.1010752},
url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
year = 2023,
month = {jan},
publisher = {Public Library of Science ({PLoS})},
volume = {19},
number = {1},
pages = {e1010752},
author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
editor = {Francis Ouellette},
title = {Galaxy Training: A powerful framework for teaching!},
journal = {PLoS Comput Biol} Computational Biology}
}

`

Congratulations on successfully completing this tutorial!