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Sunset Heroku support (#1740)

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* remove experimental heroku

* add aiohttp for dataset loading via url

* Add heroku deprecation section to docs

* remove Heroku related files from root
This commit is contained in:
Severiano Badajoz
2020-08-14 10:22:29 -07:00
committed by GitHub
parent 905308e09f
commit 018f653ec6
7 changed files with 24 additions and 117 deletions
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2
Dockerfile
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@@ -4,7 +4,7 @@ ENV LC_ALL=C.UTF-8
ENV LANG=C.UTF-8
RUN apt-get update && \
apt-get install -y build-essential libxml2-dev python3-dev python3-pip zlib1g-dev python3-requests && \
apt-get install -y build-essential libxml2-dev python3-dev python3-pip zlib1g-dev python3-requests python3-aiohttp && \
pip3 install cellxgene
ENTRYPOINT ["cellxgene"]

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Procfile
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@@ -1 +0,0 @@
web: gunicorn --chdir server/eb app:application --log-file -

29
app.json
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{
"name": "cellxgene",
"description": "An interactive explorer for single-cell transcriptomics data",
"repository": "https://github.com/chanzuckerberg/cellxgene",
"logo": "https://cellxgene-example-data.czi.technology/favicon.png",
"keywords": [
"scientific",
"visualization",
"scrna-seq",
"transcriptomics",
"dataviz"
],
"buildpacks": [
{
"url": "heroku/nodejs"
},
{
"url": "heroku/python"
}
],
"stack": "heroku-18",
"env": {
"DATASET": {
"description": "Link to dataset",
"value": "https://cellxgene-example-data.czi.technology/pbmc3k.h5ad",
"required": "true"
}
}
}

39
docs/posts/hosted.md
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@@ -38,31 +38,38 @@ If you know of other solutions, drop us a note and we'll add to this list.
# Deploying cellxgene with Heroku
## Quickstart
## Heroku Support
Clicking on the following button will forward you to Heroku to begin the deployment process:
The cellxgene team has decided to end our support for our experimental deploy to Heroku button as we move towards providing a supported method of hosted cellxgene.
<a href="https://heroku.com/deploy?template=https://github.com/chanzuckerberg/cellxgene">
<img src="https://www.herokucdn.com/deploy/button.svg" alt="Deploy">
</a>
While we no longer directly support Heroku, it is still possible to create a Heroku app via [our provided Dockerfile here](https://github.com/chanzuckerberg/cellxgene/blob/main/Dockerfile) and [Heroku's documentation](https://devcenter.heroku.com/articles/build-docker-images-heroku-yml).
If not already logged in to Heroku, there you will be prompted to log in or sign up for an account.
You may have to tweak the `Dockerfile` like so:
Once logged in you will be sent to the setup page. Here you can set some of the basic settings for the app:
```Dockerfile
FROM ubuntu:bionic
### Default settings
ENV LC_ALL=C.UTF-8
ENV LANG=C.UTF-8
- `App name`: the unique name for your deployment
- This will also serve as the default URL (e.g. https://cellxgene.herokapp.com/)
- `App owner`: Who will own this app. Either you personally or an organization/team
- `Region`: Location of the server where the app will be deployed (EU or US)
RUN apt-get update && \
apt-get install -y build-essential libxml2-dev python3-dev python3-pip zlib1g-dev python3-requests && \
pip3 install cellxgene
### Configuration
# ENTRYPOINT ["cellxgene"] # Heroku doesn't work well with ENTRYPOINT
```
- `DATASET`: A _publicly_ accessible URL pointing to a .h5ad file to view
- This defaults to pbm3k.h5ad
and provide a `heroku.yml` file similar to this:
After filling out the settings and pressing the `Deploy app` button Heroku will begin building your deployment. This process will take a few minutes, but once completed you will have a personal free hosted version of cellxgene!
```yml
build:
docker:
web: Dockerfile
run:
web:
command:
- cellxgene launch --host 0.0.0.0 --port $PORT $DATASET # the DATATSET config var must be defined in your dashboard settings.
```
## What is Heroku?

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experiments/heroku/Dockerfile
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FROM python:3.7
WORKDIR /usr/src/app
RUN pip3 install cellxgene
expose 5005

58
experiments/heroku/README.md
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@@ -1,58 +0,0 @@
# cellxgene cloud deployment with Heroku
## Quickstart
Clicking on the following button will forward you to Heroku to begin the deployment process:
<a href="https://heroku.com/deploy?template=https://github.com/chanzuckerberg/cellxgene/tree/main">
<img src="https://www.herokucdn.com/deploy/button.svg" alt="Deploy">
</a>
If not already logged in to Heroku, there you will be prompted to log in or sign up for an account.
Once logged in you will be sent to the setup page. Here you can set some of the basic settings for the app:
#### Default settings
- `App name`: the unique name for your deployment
- This will also serve as the default URL (e.g. https://cellxgene.herokapp.com/)
- `App owner`: Who will own this app. Either you personally or an organization/team
- `Region`: Location of the server where the app will be deployed (EU or US)
#### Configuration
- `DATASET`: A _publicly_ accessible URL pointing to a .h5ad file to view
- This defaults to pbm3k.h5ad
After filling out the settings and pressing the `Deploy app` button Heroku will begin building your deployment. This process will take a few minutes, but once completed you will have a personal free hosted version of cellxgene!
## What is Heroku?
Heroku is a quick and easy way to host applications on the cloud.
A Heroku deployment of cellxgene means that the app is not running on your local machine. Instead, the app is installed, configured, and ran on the Heroku servers (read: cloud).
On Heroku's servers, applications run on a [dyno](https://www.heroku.com/dynos) which are Heroku's implementation and abstraction of containers.
Heroku is one of many options available for hosting instances of cellxgene on the web.
Some other options include: Amazon Web Services, Google Cloud Platform, Digital Ocean, and Microsoft Azure.
## Why use Heroku to deploy cellxgene?
What Heroku enables is a quick, non-technical method of setting up a cellxgene instance. No command line knowledge needed. This also allows machines to access the instance via the internet, so sharing a visualized dataset is as simple as sharing a link.
Because cellxgene currently heavily relies on its Python backend for providing the viewer with the necessary data and tooling, it is currently not possible to host cellxgene as a static webpage.
This is a good option if you want to quickly deploy an instance of cellxgene to the web. Heroku deployments are free for small datasets up to around 250MBs in size. See below regarding larger datasets.
## When should I not deploy with Heroku?
- The default free dyno offered by Heroku is limited in memory to 512 MBs
- The amount of memory needed for the dyno is roughly the same size as the h5ad file
- Heroku offers tiered paid dynos. More can be found [here](https://www.heroku.com/pricing)
- Note that this can get _very_ expensive for larger datasets (\$25+ a month)
- On the free dyno, after 30 minutes of inactivity, Heroku will put your app into a hibernation mode. On the next access, Heroku will need time to boot the dyno back online.
- Having multiple simultaneous users requires more memory. This means that the free container size is easily overwhelmed by multiple users, even with small datasets; this can be addressed by purchasing a larger container size
- For this facilitated Heroku deployment to work, your dataset must be hosted on a publicly accessible URL
- By default, Heroku publically shares your instance to anyone with the URL.
- There are many ways of securing your instance. One quick and simple way is by installing [wwwhisper](https://elements.heroku.com/addons/wwwhisper), a Heroku addon

5
heroku.yml
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build:
docker:
web: experiments/heroku/Dockerfile
run:
web: cellxgene launch $DATASET --host 0.0.0.0 --port $PORT