| description |
|---|
Hosting Advice and Recipes |
Cellxgene desktop is intended to be used by researchers on their local machines. In cases where collaborators are not comfortable installing cellxgene, it is possible to host cellxgene, so your collaborators only need to open the URL you send them.
We don't officially support web deployment, but we've offered some guidance in the following sections on ways to deploy cellxgene to the web.
We are developing the Data Portal to support private sharing, however publishing is not yet widely available.
Please consider the following when deploying cellxgene in any "hosted" environment, especially where access from the broader Internet is possible:
- Information security requires careful configuration of the host environment, including firewall, logging, etc - please follow best practices
- Cellxgene includes features which may be inappropriate for a hosted deployment - you may wish to use the following command line option:
--disable-diffexp cellxgene launchcurrently uses Flask's development server, which is not recommended for hosted deployment (see the Flask documentation)- We have no testing or official support for deployments where multiple users are accessing the same cellxgene instance
- Your cellxgene instance is likely to hang or crash if too many people access it at the same time, especially if they using functions that call the Python backend (such as differential expression, noted above)
- Cellxgene only supports one instance per dataset
If you believe you have found a security-related issue with cellxgene, please report the issue immediately to security@chanzuckerberg.com.
The following configuration options require special consideration in any multi-user or hosted environment:
--disable-diffexp: the differential expression computation can be resource intensive, in particular for large datasets. If many differential expression calculation requests are made in rapid sequence, it may cause the server CPU or memory resources to be exhausted, and impact the ability of other users to access data. This command line option will disable the differential expression feature, including the removal of the Differential expression button.
--disable-annotations: annotations, which is enabled by default, may not be appropriate for hosted environments. It will write to the local file system, and in extreme cases could be used to abuse (or exceed) file system capacity on the hosting server. We recommend disabling this with this flag.
--annotations-file: this specifies a single file for all end-user annotations, and is incompatible with hosted or multi-user use of cellxgene. Using it will cause loss of user annotation data (ie, the CSV file will be overwritten). If you wish to explore using the annotations feature in a multi-user environment, please refer to the annotations documentation, and in particular the --annotations-dir flag.
There are a number of teams building tools or infrastructure to better utilize cellxgene in a multiple user environment. While we do not endorse any particular solution, you may find the following helpful.
- Novartis Cellxgene Gateway - a multiple-user and multiple-dataset gateway for cellxgene
- Interactive Environment in the Galaxy Project (patch notes)
If you know of other solutions, drop us a note and we'll add to this list.
Several groups have independently deployed various versions of cellxgene to the web. Check out the cool data that have been hosted using cellxgene!