Galaxy Monitoring with Reports
OverviewQuestions:Objectives:
How to monitor a Galaxy service with the Reports application?
Requirements:
Setup and start the Galaxy reports app.
- Galaxy Server administration
- Ansible: slides slides - tutorial hands-on
- Galaxy Installation with Ansible: slides slides - tutorial hands-on
Time estimation: 30 minutesSupporting Materials:Last modification: Sep 28, 2022
The reports application gives some pre-configured analytics screens. These are very easy to setup and can help with debugging issues in Galaxy.
Agenda
Comment: Galaxy Admin Training PathThe 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.
Setting up Reports
The reports application is included with the Galaxy codebase and this tutorial assumes you’ve already done all of the setup required for Galaxy, systemd, uWSGI, and NGINX.
Hands-on: Setup Reports
First we add a basic configuration of the Reports app to the playbook templates. Create
templates/galaxy/config/
folder, if it doesn’t exist, and createtemplates/galaxy/config/reports.yml
with the following contents:--- /dev/null +++ b/templates/galaxy/config/reports.yml @@ -0,0 +1,26 @@ +uwsgi: + socket: 127.0.0.1:9001 + buffer-size: 16384 + processes: 1 + threads: 4 + offload-threads: 2 + static-map: /static/style={{ galaxy_server_dir }}/static/style/blue + static-map: /static={{ galaxy_server_dir }}/static + static-map: /favicon.ico=static/favicon.ico + master: true + virtualenv: {{ galaxy_venv_dir }} + pythonpath: {{ galaxy_server_dir }}/lib + mount: /reports=galaxy.webapps.reports.buildapp:uwsgi_app() + manage-script-name: true + thunder-lock: false + die-on-term: true + hook-master-start: unix_signal:2 gracefully_kill_them_all + hook-master-start: unix_signal:15 gracefully_kill_them_all + py-call-osafterfork: true + enable-threads: true +reports: + cookie-path: /reports + database_connection: "{{ galaxy_config.galaxy.database_connection }}" + file_path: /data + filter-with: proxy-prefix + template_cache_path: "{{ galaxy_mutable_data_dir }}/compiled_templates"
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:
- Ignore the header
- Remove lines starting with - from your file
- 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 @@
-🍎
-🍐
-🍊
-🍋
-🍒
-🥑In your
galaxyservers
group variables file, tell the playbook to deploy the reports configuration file:--- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -51,6 +51,7 @@ galaxy_root: /srv/galaxy galaxy_user: {name: galaxy, shell: /bin/bash} galaxy_commit_id: release_22.05 galaxy_force_checkout: true +galaxy_reports_path: "{{ galaxy_config_dir }}/reports.yml" miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" miniconda_version: 4.7.12 miniconda_manage_dependencies: false @@ -131,6 +132,8 @@ galaxy_config_templates: dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" - src: templates/galaxy/config/tool_destinations.yml dest: "{{ galaxy_config.galaxy.tool_destinations_config_file }}" + - src: templates/galaxy/config/reports.yml + dest: "{{ galaxy_reports_path }}" galaxy_local_tools: - testing.xml
Similar to Galaxy we will again use systemd to manage the Reports process.
--- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -144,6 +144,7 @@ galaxy_dynamic_job_rules: # systemd galaxy_manage_systemd: true +galaxy_manage_systemd_reports: yes galaxy_systemd_env: [DRMAA_LIBRARY_PATH="/usr/lib/slurm-drmaa/lib/libdrmaa.so.1"] # Certbot
Then we need to tell NGINX it should serve our Reports app under
<server_url>/reports
url. Edit yourtemplates/nginx/galaxy.j2
file, and within the server block, add a block for proxying the reports application. It should look like:--- a/templates/nginx/galaxy.j2 +++ b/templates/nginx/galaxy.j2 @@ -105,4 +105,10 @@ server { uwsgi_param UWSGI_SCHEME $scheme; include uwsgi_params; } + + location /reports/ { + uwsgi_pass 127.0.0.1:9001; + uwsgi_param UWSGI_SCHEME $scheme; + include uwsgi_params; + } }
Run the playbook:
Input: Bashansible-playbook galaxy.yml
The reports application should be available, under
<server_url>/reports/
.>
1.sh
Comment: Insecure!But notice that your Reports server is not secured! Check out the External Authentication tutorial for information on securing Reports.
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
Galaxy supports pluggable monitoring extensions.
The Reports webapp is one option to monitor your system.
Frequently Asked Questions
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 ForumFeedback
Did you use this material as an instructor? Feel free to give us feedback on how it went.
Did you use this material as a learner or student? Click the form below to leave feedback.
Citing this Tutorial
- Nate Coraor, Björn Grüning, Simon Gladman, Helena Rasche, 2022 Galaxy Monitoring with Reports (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/reports/tutorial.html Online; accessed TODAY
- Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012
Congratulations on successfully completing this tutorial!@misc{admin-reports, author = "Nate Coraor and Björn Grüning and Simon Gladman and Helena Rasche", title = "Galaxy Monitoring with Reports (Galaxy Training Materials)", year = "2022", month = "09", day = "28" url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/reports/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} }