inst/scripts/Readme.md

In grimbough/rhdf5: R Interface to HDF5

Description

This folder contains the script used to produce the example HDF5 files found in the inst/testfiles/ folder. These are created using the reference implementation of the anndata library found in anndata.

Generating the data

Using Docker

If you do not have a version of python and zarr readily available, you can alternatively use the Dockerfile provided to generate the data. The following command will build a container called zarr_tester.

docker build -t anndata-nullable .   

To generate the data you then use the command below. This will produce the example files in the folder /tmp/zarr on your local filesystem. Modify that path in the call to docker run if it is not appropriate for your system.

mkdir /tmp/anndata-nullable
docker run --rm --name anndata-nullable --user ${UID}:${UID} \
  -v /tmp/anndata-nullable:/data \
  anndata-nullable

grimbough/rhdf5 documentation built on Jan. 11, 2025, 5:32 a.m.