Galaxy Monitoring with Reports

Authors: AvatarNate Coraor orcid logoAvatarBjörn Grüning AvatarSimon Gladman orcid logoAvatarHelena Rasche
Overview
Questions:

  • How to monitor a Galaxy service with the Reports application?

Objectives:

  • Setup and start the Galaxy reports app.

Requirements:
Time estimation: 30 minutes
Supporting Materials:
Last modification: Sep 28, 2022
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License The GTN Framework is licensed under MIT

The reports application gives some pre-configured analytics screens. These are very easy to setup and can help with debugging issues in Galaxy.

Agenda
  1. Setting up Reports
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

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

  1. 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 create templates/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:

    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. 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

  3. 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

  4. Then we need to tell NGINX it should serve our Reports app under <server_url>/reports url. Edit your templates/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;
+    }
 }

  5. Run the playbook:

    Input: Bash
    ansible-playbook galaxy.yml

  6. The reports application should be available, under <server_url>/reports/.>

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 Forum

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Citing this Tutorial

  1. 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
  2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012 


@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}
}

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