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Cellxgene Command Line Arguments
The command line arguments for cellxgene vary slightly between different versions. This poses a challenge for cellxgene-gateway, which could be asked to launch any version of cellxgene (potentially with the VIP plugin).
- GATEWAY_ENABLE_ANNOTATIONS - defaults to false, enables annotations in cellxgene gateway when either "new" or existing annotation clicked in UI
- CELLXGENE_ARGS - additional arguments to be passed into all cellxgene invocations
The 0.3.7 release of cellxgene-gateway was tested with cellxgene 0.19.0. This version of cellxgene supports three kinds of arguments
- --annotations-file (Incompatible with --user-generated-data-dir.)
- --gene-sets-file (Incompatible with --user-generated-data-dir.)
- --user-generated-data-dir (Incompatible with --annotations-file and --gene-sets-file)
- --annotations-dir older synonym of --user-generated-data-dir, used by cellxgene gateway if the annotation item descriptor returns an empty path. It creates an annotations directory by removing the ".h5ad" and adding "_annotations".
- --disable-annotations (Otherwise user will be prompted to enter annotations.
The annotations functionality supported by 0.3.7 makes use of the --annotations-file argument if an annotation file is desired, or otherwise the --disable-annotations argument. Versions of cellxgene older than 0.16.8 are not being tested, and may throw errors if they do not support these two annotations. Here are some examples of when the different arguments are passed to cellxgene:
- http://localhost:5005/view/pbmc3k.h5ad/ - in this case, an h5ad file is specified, so --disable-annotations is passed
- http://localhost:5005/view/pbmc3k_annotations/m56.csv/ - in this case, an annotation file is specified, so --annotations-file is passed
- http://localhost:5005/view/pbmc3k_annotations/ in this case, a directory is specified, so --annotations-dir could be passed. This is not currently supported by the FileItemSource.
The most recent version of the VIP Plugin uses 0.16.8, which does not support --gene-sets-file. It may be desirable to support gene-sets-file at some point, but this may require an environment variable of some kind to enable compatibility with Cellxgene VIP.