SENTSeqDB: LaminDB module for SENTSeq

Installation

pip install git+https://github.com/laminlabs/sentseqdb

sentseq-track CLI

Usage: sentseq-track [OPTIONS] COMMAND [ARGS]...

Options:
  --version        Show the version and exit.
  --help     -h    Show this message and exit.

Commands:
  align            Run the SENTseq align tracking.
  preprocess       Run the SENTseq preprocess tracking.

python API

  • Guide walks through usage (notebooks are run in CI)

  • Reference provides the API reference

  • Notes documents static notebooks

  • Changelog lists changes

Running on AWS-lambda

Environment variables:

  • LAMIN_CACHE_DIR: a writable directory. This is the environment variable that sets cache directory for lamindb.

  • BENCHLING_BASE_URL: required for registering metadata from Benchling.

    • https://navatx.benchling.com/ (prod)

    • https://navatxtest.benchling.com/ (test, likely not contain the corresponding metadata, only use for testing)

  • One of the following Benchling credentials:

    • BENCHLING_CLIENT_ID and BENCHLING_CLIENT_SECRET

    • BENCHLING_API_KEY