Galaxy Interactive Tools

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# Galaxy Interactive Tools

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<ul class="text-list">
			
			<li>
				
  <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/eancelet/" class="contributor-badge contributor-eancelet"><img src="https://avatars.githubusercontent.com/eancelet?s=36" alt="Estelle Ancelet avatar" width="36" class="avatar" />
    Estelle Ancelet</a>
  
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  <a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
    Anthony Bretaudeau</a>
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???
Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

Press `P` again to switch presenter notes off

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This window is linked to the main window. Changing slides on one will cause the
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Useful when presenting.

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn the differences between Galaxy Interactive Environments and Galaxy Interactive Tools

- Have an understanding of what Galaxy Interactive Tools are and how they work

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# History

## 2015

@hexylena, @bgruening, and @jmchilton create Galaxy Interactive Environments (GIEs)

GIEs use Galaxy's *visualization framework* to run certain types of *interactive* visualizations (e.g. Jupyter Notebook)

GIEs run in a docker container on the Galaxy server or a single remote Docker server

???

- Galaxy Interactive Environments were added to Galaxy in 2015.
- They are a type of visualization in Galaxy.
- Accessible through the “Visualize” menu or under the visualization button on a dataset with a specific datatype.
- Back then, the docker container serving an interactive environment could not be run on a cluster.
- More details within Galaxy Interactive Environment slides.

---
# History

## 2016

Support for Docker Swarm is added, allowing running a cluster for GIEs

???

- As of 2016, Docker includes swarm mode for natively managing a cluster of Docker Engines called a swarm.
- This allowed to run Galaxy Interactive Environment on a cluster.

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# History

## 2019

@blankenberg creates Galaxy Interactive Tools (GxITs)

Building on the GIE concept, but run as *tools*

Tools run just as any other Galaxy job (e.g. via Slurm, HTCondor)

You will sometimes see Interactive Tools referred to as Interactive Environments version 2

???

- In 2019, were created the Galaxy Interactive Tools.
- Like interactive environment, Galaxy Interactive Tools are built on docker containers and are accessible through the Galaxy interface.
- But they are considered as tools.
- They are launchable from the toolbox menu, on a predefined destination and prioritized as any other job.

---
# Tool config syntax

```xml
<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook" version="0.1">
    <requirements>
        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:ie2</container>
    </requirements>
    <entry_points>
        <entry_point name="Jupyter Interactive Tool" requires_domain="True">
            <port>8888</port>
            <url>ipython/lab</url>
        </entry_point>
    </entry_points>
</tool>
```

???

- Some settings are needed to configure an interactive tool wrapper.
- The tool type must be set to interactive.
- As a requirement, set the path to the repository where the container is to be pulled from.
- The tool entry point on the container must be defined.
- For instance, for a Jupyter Notebook, you'll give the port the application is served on and the domain name suffix.

---
# Mapping clients to containers

- GIEs: Unique path, e.g. `https://galaxy.example.org/gie-proxy/jupyter/...`
  - Pros: Works with existing SSL certificate
  - Cons: Requires Galaxy session cookie (no sharing), can only run one at a time, closing your browser loses your session
- GxITs: Unique hostname, e.g. `https://<unique-id>.ep.interactivetool.galaxy.example.org/`
  - Pros: Needs no special credentials (can be shared)
  - Cons: Requires *wildcard* DNS entry and *wildcard* SSL certificate (not possible at many sites)

???

- Diverse infrastructures behind Galaxy Interactive Environments and Galaxy Interactive Tools induces various constraints and benefits.
- Particularly in building the path between the browser and the container.

---
# Anatomy of a running Interactive Tool

![Galaxy Interactive Tools Proxy Diagram](../../images/interactive-tools/gxit-proxy-diagram.png "Galaxy Interactive Tools Proxy Diagram")

.reduce70[.footnote[The source for this figure can be found at: https://docs.google.com/presentation/d/1_4PtfM6A4mOxOlgGh6OGWvzFcxD1bdw4CydEWtm5n8k/]]

???

- This slide illustrates the steps allowing a client to interact with a Galaxy Interactive Tool.
- We consider a Galaxy server running behind a reverse proxy (NGINX).
- The client only ever speaks to NGINX on the Galaxy server, running on the standard HTTPS 443 port.
- Based on the elements provided by the URL, NGINX redirects the requests to Galaxy over a unix domain socket as usual.
- On the other hand, HTTP requests targetting interactive tools are redirected by NGINX to a proxy, called GIE Proxy, running on port 8000.
- At this point, remember, when an docker container starts, it will be assigned a host (server or node) and a random port on that host (in our example, port 32768).
- This information is stored by Galaxy in a sqlite database.
- So the GIE proxy checks in this sqlite database to know which node and port the IT container is to be found.
- The GIE proxy forwards the HTTP request to Docker on that node and port.
- Docker, in turn, forwards it to the application (e.g. Jupyter) on the container's port, defined in the wrapper.

---
# Galaxy configuration

Enable docker on a destination in `job_conf.xml` and assign your GxITs to that destination

.left[Set in `galaxy.yml`:]
```yaml
interactivetools_enable: true
interactivetools_map: /srv/galaxy/var/gie-proxy-sessions.sqlite
```

???

- A few settings are needed to get interactive tools running within your Galaxy instance.
- In your galaxy configuration file, enable the use of interactive tools then set the path to the sqlite database storing the proxying data.
- In the job configuration file, give to the tool a destination allowing the use of Docker (more details in the tutorial).

---
# Proxy configuration

Use the proxy configuration that ships with Galaxy

Or the [Node.js-based proxy][usegalaxy_eu-gie_proxy]

[usegalaxy_eu-gie_proxy]: https://galaxy.ansible.com/usegalaxy_eu/gie_proxy

???

- In production, you are likely to use the Node.js based proxy, set up by the Galaxy admin team.
- During developement, you can use the proxy configuration used by default by Galaxy.

---
# Security

The default docker-enabled container exposes all datasets to the tool

Normally this isn't bad (normal tools can't be controlled by the user)

Interactive tools are fully user controllable

Solution: [Embedded Pulsar][job-conf-pulsar-embedded]

[job-conf-pulsar-embedded]: https://github.com/galaxyproject/galaxy/blob/6622ad1acb91866febb3d2f229de7cfb8af3a9f6/lib/galaxy/config/sample/job_conf.xml.sample_advanced#L106

???

- As we have seen, interactive tools are launched in docker containers.
- By default in galaxy, each container has full access to all user's data.
- This is a security issue since a user could take control of an interactive tool and read, write or delete those data.

---
# Embedded Pulsar

Runs a [Pulsar][pulsar] server within the Galaxy application to "stage" (i.e. copy) inputs.

- Pros: Inputs in isolated dir so only that dir is mounted in the container: secure
- Cons: Has to copy inputs on each Interactive Tool execution: slow

[pulsar]: https://github.com/galaxyproject/pulsar

???

- A solution to this security issue is to use embedded pulsar.
- This way, pulsar makes available only the job input data to the container.
- Moreover, these data are read only.
- You will have more details in the tutorial.

---

## 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!

<div class="contributors-line">
		
<table class="contributions">
	
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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>
		<td>
			
  <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/eancelet/" class="contributor-badge contributor-eancelet"><img src="https://avatars.githubusercontent.com/eancelet?s=36" alt="Estelle Ancelet avatar" width="36" class="avatar" />
    Estelle Ancelet</a>
  
  <a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
    Anthony Bretaudeau</a>
  
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			
  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge 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/slugger70/" class="contributor-badge contributor-slugger70">
    <img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena">
    <img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-nsoranzo">
    <img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud">
    <img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
  </a>
  
  <a href="/training-material/hall-of-fame/martenson/" class="contributor-badge contributor-martenson">
    <img src="https://avatars.githubusercontent.com/martenson?s=36" alt="Martin Čech avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/eancelet/" class="contributor-badge contributor-eancelet">
    <img src="https://avatars.githubusercontent.com/eancelet?s=36" alt="Estelle Ancelet avatar" width="36" class="avatar" />
  </a>
  
  <a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann">
    <img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" />
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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/>