Galaxy Administrator Time Burden and Technology Usage
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##Context
Context
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- Have you wondered how difficult Galaxy is to run? How much time people must spend to run Galaxy?
- In February 2024, we collected 9 responses from the Galaxy Small Scale Admin group
- Questions about various time burdens and technological choices
- Full version of the report, + form export
- Raw data (anonymised) + analysis script ]
Overview of Participants’ Galaxy Instances’
Active Users
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- 3 categories : <10, circa 20 & circa 50
- Active vs signed up: no problem having a lot more signed up than active users, no need to delete inactive users (in case they come back) ]
Computing Method
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- Admins generally use a batch scheduler (often HTCondor)
- Some admins use Pulsar to send jobs to remote machines
- And a few use the local scheduler which will not survive a machine restart. ]
Object Store Backend
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- Local storage (SSD/HDDs attached to the machine) and NASs are popular options for data storage
- S3 is a less common option amongst small scale admins
- You can use whatever storage you have available ]
Ansible Usage
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.pull-right[ Is a highly-used (about 80%) tool that, according to the other sections, greatly simplifies admin. ]
Gravity Usage
- Since Galaxy 23.0, Gravity is used to manage Galaxy processes
- If you use Ansible to setup Galaxy, this process is mostly transparent, and you may not know you’re using Gravity
User Support & Training
End-User Support Burden
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- 1 hour per week average end-user support
- Lots of training (though that’s part of the next question)
- Lots of developing &/or debugging users’ tools/workflows for them. ]
User Training Burden
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- 1 hour per week average user training
- Usually makes use of existing Galaxy tutorials, sometimes in-person
- The tutorials aren’t always specific enough, requiring some custom Q&A ]
Tool & Workflow Dev & Maintenance
User Tool Dev & Planemo Usage
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- Users developing their own tools is rare, and if they do, they rarely use Planemo.
- Tool creation is actually mostly done through copy/pasting XMLs
- Planemo shines when it comes to tool testing, linting and publishing ]
Admin Workflow Dev Burden
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- The administrative burden of running Galaxy is highly variable
- On average admins spend 4 hours a month managing Galaxy ]
Admin Tool Dev Planemo
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- Many small scale Galaxy admins will find themselves responsible for developing tools
- Amongst tool-developing admins, 5/7 use Planemo
- Planemo is a useful tool for tool testing, linting and publishing tools for your local Galaxy ]
Admin Tool Dev Creation Burden
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.pull-right[ Small (1 hour per week avg.) amount of tool dev per month. ]
Admin Tool Dev Updating Burden
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- Excluding the extreme values, about an hour a month
- I wondered if tools became invalid because of non-backwards-compatible format changes, but that does not seem to be the case ]
##Tool Storage & Packaging
Admin Tool Dev Storage
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- Most tools are files on the same machine as Galaxy
- Some tools are used from public toolsheds, none from private ones
- Currently, admins write the tool (managed in git), test & lint it with Planemo, then publish it locally, sometimes versioned (ex: tool_v1.1) ]
Tool Dev Packaging Method
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.pull-right[ Lots of Conda, a few containers. ]
Tool Dev Packaging Burden
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- Admins generally spend very little time managing conda environments in Galaxy.
- Galaxy can automatically create and manage conda environments for every installed tool ]
Database-related Characteristics & Tasks
DB Tech
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- It is strongly recommended to use PostgreSQL in production ]
DB Schema Update Frequency
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- Happens on average once a year.
- If Galaxy is managed with Ansible, this happens automatically as part of updating Galaxy. ]
DB Schema Update Duration
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.pull-right[ Is very quick and transparent (assuming Ansible usage) ]
DB Backup Frequency
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- Many admins keep one (point in time) backup per week
- The Ansible role Galaxy uses for Postgres can be used to configure both point in time recovery or WAL backups.
- The general Galaxy DB Admin tutorial covers how to setup backups. ]
Galaxy Version & Upgrades
Current Version & Upgrade Frequency
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- Half the respondents are able to continue using a version that is 2-3 years old
- This is not recommended as versions older than a year do not receive security updates
- But most update about once a year ]
Galaxy Upgrades Duration (excluding DB schema migration duration)
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- Avg 3 hours, big variance, which doesn’t seem proportional to the amount of users, but rather other factors
- Some updates are very simple, especially if you use Ansible
- Some non-backwards-compatible changes like uWSGI to Gunicorn take longer, but these changes are not a regular occurrence in Galaxy.
- Some admins take longer because of custom plugins (that need to be updated) or test deployment environments that need to be maintained. ]
##Miscellaneous: Restarts, Crashes & Other
Intentional Restarts Frequency
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- If you configure Galaxy to use a job scheduler (SLURM, HTCondor, etc), restarts will not interrupt existing jobs.
- Generally admins restart about once a month, in order to apply system updates or reconfigure Galaxy or its tools
- Some Galaxy / tools reconfiguration is possible without restarting ]
Crashes Frequency
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- Avg. once every 3-4 months
- Causes: Storage space full, or access rights problems, or very rarely TUS (but a solution was found for this since the poll (see the full report)) ]
Other Recurrent Tasks Duration
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- 3h per month avg
- Cleaning “paused” jobs
- Adjusting user quotas & notifying users
- Networking with other admins
- Troubleshooting tools
- Testing new Galaxy versions
- Custom welcome-pages ]
##Take Home
Total Burden, Non-Dev Admin Tasks
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- Per month: circa 15 hours
- Per week: half a working day
- Reasonable amount
- Actually slightly less because there is some overlap in user training between the “End-user support” and “User training” questions ]
Thank you!
This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!![page logo](/training-material/assets/images/gat.png)