diff --git a/dev_docs/cxg.md b/dev_docs/cxg.md index e851692f..05bf465f 100644 --- a/dev_docs/cxg.md +++ b/dev_docs/cxg.md @@ -1,3 +1,5 @@ +## UPDATE (9/30/2020): Starting today, the name Corpora will only be used as the internal project name, with cellxgene Data Portal being the official product name + # CXG Data Format Specification Document Status: _draft_ diff --git a/docs/_config.yml b/docs/_config.yml index 8ac27944..f70c05b5 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -15,6 +15,8 @@ nav: url: posts/gallery - title: Demo datasets url: posts/demo-data + - title: All other datasets + url: https://cellxgene.cziscience.com/ - title: Preparing your data url: posts/prepare - title: Launching cellxgene @@ -33,5 +35,3 @@ nav: url: posts/contribute - title: Contact & finding help url: posts/contact - - title: cellxgene.cziscience.com - url: posts/cellxgene_cziscience_com diff --git a/docs/_site/index.html b/docs/_site/index.html index 2a5ed4f1..42326a08 100644 --- a/docs/_site/index.html +++ b/docs/_site/index.html @@ -7,19 +7,19 @@ Index | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Index","name":"cellxgene","description":"An interactive explorer for single-cell transcriptomics data","@type":"WebSite","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/annotations.html b/docs/_site/posts/annotations.html index 2a76ec9f..725ab7db 100644 --- a/docs/_site/posts/annotations.html +++ b/docs/_site/posts/annotations.html @@ -7,19 +7,19 @@ annotations | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/annotations.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"annotations","description":"Creating annotations","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/contact.html b/docs/_site/posts/contact.html index 33c31b51..2bbefffa 100644 --- a/docs/_site/posts/contact.html +++ b/docs/_site/posts/contact.html @@ -7,19 +7,19 @@ Contact | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/contact.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Contact","description":"Contact","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/contribute.html b/docs/_site/posts/contribute.html index 494d2ca3..9727cffb 100644 --- a/docs/_site/posts/contribute.html +++ b/docs/_site/posts/contribute.html @@ -7,19 +7,19 @@ Code of conduct | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/contribute.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Code of conduct","description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/demo-data.html b/docs/_site/posts/demo-data.html index 479e6249..4b05dfbe 100644 --- a/docs/_site/posts/demo-data.html +++ b/docs/_site/posts/demo-data.html @@ -7,19 +7,19 @@ demo-data | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/demo-data.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"demo-data","description":"Demo datasets","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/gallery.html b/docs/_site/posts/gallery.html index 2321d81e..5b19ba47 100644 --- a/docs/_site/posts/gallery.html +++ b/docs/_site/posts/gallery.html @@ -7,19 +7,19 @@ Gallery | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/gallery.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Gallery","description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

@@ -130,7 +130,7 @@ Check out the cool data that our users are using cellxgene to explore!

Melanoma

-

CZI’s own cellxgene site

+

CZI’s own cellxgene site

Want us to link to your dataset here? Just send us a note!

diff --git a/docs/_site/posts/hosted.html b/docs/_site/posts/hosted.html index 0e2d2b6a..b85e5d96 100644 --- a/docs/_site/posts/hosted.html +++ b/docs/_site/posts/hosted.html @@ -7,19 +7,19 @@ Hosting cellxgene on the web | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/hosted.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Hosting cellxgene on the web","description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

@@ -139,35 +139,36 @@

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.

-

- Deploy -

+

While we no longer directly support Heroku, it is still possible to create a Heroku app via our provided Dockerfile here and Heroku’s documentation.

-

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:

+
FROM ubuntu:bionic
 
-
Default settings

+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 && \
+    pip3 install cellxgene
 
-
Configuration

+# ENTRYPOINT ["cellxgene"]  # Heroku doesn't work well with ENTRYPOINT
+
- +

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!

+
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?

diff --git a/docs/_site/posts/hosted.md b/docs/_site/posts/hosted.md index 1168bdf0..073ede26 100644 --- a/docs/_site/posts/hosted.md +++ b/docs/_site/posts/hosted.md @@ -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. - - Deploy - +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? diff --git a/docs/_site/posts/install.html b/docs/_site/posts/install.html index 2eb470d8..649209dc 100644 --- a/docs/_site/posts/install.html +++ b/docs/_site/posts/install.html @@ -7,19 +7,19 @@ Install | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/install.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Install","description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/launch.html b/docs/_site/posts/launch.html index 4aed95b3..86c8dd3b 100644 --- a/docs/_site/posts/launch.html +++ b/docs/_site/posts/launch.html @@ -7,19 +7,19 @@ demo-data | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/launch.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"demo-data","description":"Demo datasets","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/methods.html b/docs/_site/posts/methods.html index 8c97a84c..f27e270e 100644 --- a/docs/_site/posts/methods.html +++ b/docs/_site/posts/methods.html @@ -7,19 +7,19 @@ Methods | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/methods.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Methods","description":"An interactive explorer for single-cell transcriptomics data","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/prepare.html b/docs/_site/posts/prepare.html index 56dce0c2..2b3b0f05 100644 --- a/docs/_site/posts/prepare.html +++ b/docs/_site/posts/prepare.html @@ -7,19 +7,19 @@ prepare | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/prepare.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"prepare","description":"Preparing your data","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/roadmap.html b/docs/_site/posts/roadmap.html index 34dc26b9..837a3bb7 100644 --- a/docs/_site/posts/roadmap.html +++ b/docs/_site/posts/roadmap.html @@ -7,19 +7,19 @@ roadmap | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/roadmap.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"roadmap","description":"Roadmap","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/_site/posts/troubleshooting.html b/docs/_site/posts/troubleshooting.html index a936237a..c43ee9af 100644 --- a/docs/_site/posts/troubleshooting.html +++ b/docs/_site/posts/troubleshooting.html @@ -7,19 +7,19 @@ Troubleshooting | cellxgene - + - - + + +{"url":"http://localhost:4000/cellxgene/posts/troubleshooting.html","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"http://localhost:4000/cellxgene/cellxgene-logo.png"}},"headline":"Troubleshooting","description":"Troubleshooting","@type":"WebPage","@context":"https://schema.org"} - + @@ -50,6 +50,10 @@ + All other datasets
+ + + Preparing your data
@@ -85,10 +89,6 @@ Contact & finding help
- - cellxgene.cziscience.com
- - Code

diff --git a/docs/posts/cellxgene_cziscience_com.md b/docs/deprecated/cellxgene_cziscience_com.md similarity index 100% rename from docs/posts/cellxgene_cziscience_com.md rename to docs/deprecated/cellxgene_cziscience_com.md diff --git a/docs/posts/gallery.md b/docs/posts/gallery.md index 13a7fc24..01f45301 100644 --- a/docs/posts/gallery.md +++ b/docs/posts/gallery.md @@ -39,6 +39,6 @@ Check out the cool data that our users are using cellxgene to explore! ### [Melanoma](https://melanoma.cellgeni.sanger.ac.uk/) -### [CZI's own cellxgene site](cellxgene_cziscience_com) +### [CZI's own cellxgene site](https://cellxgene.cziscience.com/) _Want us to link to your dataset here? [Just send us a note!](contact)_