This python module performs the task of adding 10xgenomics data to the celldb functional genomics server.

This is done by providing the location of an HDF5 found that has either been mounted to the Dockerfile, or available on the filesystem.

To load your data into celldb using python, install the module and then direct it at a celldb host, and a 10xgenomics h5 file.

pip install celldb-etl-10x
celldb_etl_10x localhost my_10x_data.h5

10xgenomics data are organized by barcode, which are considered the sample's unique identifier in celldb. If you expect to load a very large amount of samples consider adding a "salt" to the identifiers. This will append a small string to each identifier to help guarantee uniqueness across datasets. The salt is provided by the hash of the upsert statement used to create the row, to help reduce duplication.

pip install celldb-etl-10x
celldb_etl_10x localhost my_10x_data.h5 --salt

If you would like to load a 10xgenomics data file using a docker instance, first try:

docker run -it david4096/celldb-etl-10x celldb_etl_10x localhost my_10x_data.h5

This will run a docker container and print logs to the terminal. If no arguments are provided 20k cells from the 10xgenomics Megacell demonstration will be downloaded.