Galaxy from an administrator's point of view

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# Galaxy from an administrator's point of view

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				<a href="/training-material/hall-of-fame/valentinmarcon/" class="contributor-badge contributor-valentinmarcon"><img src="https://avatars.githubusercontent.com/valentinmarcon?s=36" alt="Valentin Marcon avatar" width="36" class="avatar" />
    Valentin Marcon</a>
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				<a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
    Nate Coraor</a>
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				<a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a>
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				<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a></li>
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![Picture with 125+ platforms for using galaxy written and a number of screenshots of those galaxies.](../../images/use-resource-banner.png)

---

# Where can Galaxy run?

* Cloud (SaaS)
  - A usegalaxy.* site: [Galaxy Australia](https://usegalaxy.org.au), [Galaxy Europe](https://usegalaxy.eu), [Galaxy France](https://usegalaxy.fr), [Galaxy Main](https://usegalaxy.org)
  - [Public Galaxy Servers](https://galaxyproject.org/use)
  - [Amazon EC2 or MS Azure](https://launch.usegalaxy.org/)
  - Semi-private cloud (e.g.: [NeCTAR](https://nectar.org.au/), [Jetstream](http://jetstream-cloud.org/))
* Private cloud (build your own Galaxy SaaS)
* Cloud (IaaS)
  - Any cloud
* Scalable Local Server
  - Dedicated or shared compute cluster(s)
  - Cloud compute resources
* Standalone Local Server

---

# Choosing where to run

[Resource Directory](https://galaxyproject.org/use/)

Supported                                         | UseGalaxy.* | Local     | Cloud
---------                                         | ----        | -----     | -----
Moderate Data                                     | ✅          | ✅        | ✅
Big Data                                          | ❌          | 🤷‍♀️ | ✅
Moderate Computations                             | ✅          | ✅        | ✅
Long/Expensive Computations                       | ❌          | 🤷‍  | ✅
You want to share your Galaxy objects with others | ✅          | ✅        | ✅
All needed Tools are pre-installed                | ✅          | 🤷‍♂️ | ✅
Human Data / Proprietary Data                     | ❌          | ✅        | ✅
No network transfer of data                       | ❌          | ✅        | ❌

---

## Reasons to Install Your Own Galaxy

- You want to run a local [production Galaxy](https://docs.galaxyproject.org/en/latest/admin/production.html)
- You want to develop [Galaxy tools](https://galaxyproject.org/admin/tools/add-tool-tutorial)
- You want to [Develop Galaxy](https://galaxyproject.org/develop/) itself
- [Install](https://galaxyproject.org/admin/tools/add-tool-tutorial) and use tools unavailable on [public Galaxies](https://galaxyproject.org/public-galaxy-servers)
- Use sensitive data (e.g. clinical)
- Process large datasets that are too big for public Galaxies
- [plug-in](https://galaxyproject.org/admin/internals/data-sources) new datasources

---

# Software Requirements

Required:
  - Galaxy is written in Python and depends on **Python 3.8** or newer

Minimal [production](https://docs.galaxyproject.org/en/master/admin/production.html) requirements:
  - [PostgreSQL](/training-material/topics/admin/tutorials/database/slides.html)
  - Reverse proxy server (NGINX, Apache)

---

# Hardware Requirements

This depends:

- What do you intend to run?
- Where do you intend to run it?

If possible, run the Galaxy server **separate** from Galaxy jobs

**Storage** will usually be the biggest concern

???

- Depends on your available infrastructure
- If you are storage limited, can be addressed by policy of deleting old/unused histories
- If you are compute limited, can be addressed with queue limits

---
# Server Hardware Requirements

Based on concurrent user count and assuming separate compute for jobs:

Users     | Resource estimate
----------|-------------------
1 - 5     | 1 core, 1GB, 10 TB
5 - 20    | 2 cores, 2 GB, 40 TB
20 - 40   | 8 cores, 8 GB, 200 TB
40+       | multiple hosts, 16 GB/host, 500 TB, dedicated DB host

Storage is more difficult to estimate since it is, like compute, **analysis** and **policy** dependent

---
template: left-aligned

# Galaxy Storage Philosophy

- Foster transparency and reproducibility
- Data is always created, *never overwritten*
- Copying history or library datasets associate them with the original file on disk without an actual copy
- By default, data is never really deleted unless *explicitly instructed*
- Even deleted data can be undeleted unless *forcibly purged*

---

# Storage Requirements

An "average" 2018 NGS analysis (by Anton Nekrutenko): **66 GB**

10 users, 10 histories: **> 6 TB**

Solutions:

- Quotas
- Set job limits in the job conf
- Clean up deleted data (with a cron job)
- Forced removal based on age
- Users can configure their workflows to delete intermediate tool outputs
- Data libraries for common data
- Public servers: require email verification (and watch for duplicates)
- Plug in more/heterogeneous storage using Object Store configuration

---

# Compute Requirements

This depends:

- What tools will your users be using?
  - What are their requirements?
- In general, the most commonly used tools use a single core
  - But can use lots of memory!
- Some compute-intensive tools use multiple cores

usegalaxy.org allocates from **8 GB/core** to **16 GB/core**

Connecting Galaxy to clusters/HPC is covered in the advanced section.

---

# Making plans

**Before** deploying your first Galaxy server:

- Figure out where Galaxy will be stored
  - Make sure it will be accessible to any eventual compute
- Figure out where data will be stored
  - Make sure it will be accessible to any eventual compute

---

# Galaxy deployment options

- As developer: `git clone https://github.com/galaxyproject/galaxy.git`
- Ready-to-use locally: [Docker](https://github.com/bgruening/docker-galaxy-stable/)
- Production server: configuration management (e.g. Ansible)

In future:

- Alternative to git clone: Galaxy wheel in PyPI

---

# Deployment Best Practices

- **Use configuration management**
  - [Ansible](http://docs.ansible.com) for which Galaxy Project maintains roles ([tutorial](https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible/slides.html))
  - Other systems are possible (Chef, Puppet, SaltStack, CFEngine) but do not have project-maintained roles.

- Whether you use configuration management or not, *record every change you make on a version control system* (e.g. git):
  - Large, complex deployments grow organically
  - If you don't know what you did, you can't do it again

---

# System Administration Best Practices

- Take security seriously
- **Update Galaxy when security updates are released**
- Follow OS security best practices
- Privilege separate code/job/data ownership
- Write protect Galaxy and data if you can
- Read-only cluster mounts

Back up everything (except that which is managed by configuration management)

---

## Related tutorials

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
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			<a href="/training-material/hall-of-fame/valentinmarcon/" class="contributor-badge contributor-valentinmarcon"><img src="https://avatars.githubusercontent.com/valentinmarcon?s=36" alt="Valentin Marcon avatar" width="36" class="avatar" />
    Valentin Marcon</a><a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
    Nate Coraor</a><a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a><a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a>
		</td>
	</tr>

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		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
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			<a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-badge-small contributor-slugger70"><img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/bebatut/" class="contributor-badge contributor-badge-small contributor-bebatut"><img src="https://avatars.githubusercontent.com/bebatut?s=36" alt="Bérénice Batut avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-badge-small contributor-natefoo"><img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-badge-small contributor-hexylena"><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/mtekman/" class="contributor-badge contributor-badge-small contributor-mtekman"><img src="https://avatars.githubusercontent.com/mtekman?s=36" alt="Mehmet Tekman avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-badge-small contributor-shiltemann"><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-badge-small contributor-nsoranzo"><img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-badge-small contributor-bgruening"><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/gallardoalba/" class="contributor-badge contributor-badge-small contributor-gallardoalba"><img src="https://avatars.githubusercontent.com/gallardoalba?s=36" alt="Cristóbal Gallardo avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/willdurand/" class="contributor-badge contributor-badge-small contributor-willdurand"><img src="https://avatars.githubusercontent.com/willdurand?s=36" alt="William Durand avatar" width="36" class="avatar" /></a></td>
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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>