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Run an example of a configuration using environment variable tokens

Environment variables and configuration tokens describes how the use of configuration tokens representing environment variables with their paths, and the use of symbolic links are supported. This page walks you through a runnable example, using the "vignette" dataset from Map mRNA and ribosome protected reads to transcriptome and collect data into an HDF5 file.

Create and populate data, organisms, and samples directories:

$ cp -r riboviz/data/ ribo-data
$ mkdir ribo-organisms
$ cp riboviz/vignette/input/yeast_* ribo-organisms/
$ mkdir -p ribo-samples/input
$ cp riboviz/vignette/input/SRR10428* ribo-samples/input/

Create a directory with a configuration file:

$ mkdir ribo-run/
$ cp riboviz/vignette/riboviz_env.yaml ribo-run
$ cd ribo-run

riboviz_env.yaml is a sample configuration, based on vignette_config.yaml but with tokens for paths to the input files expected by riboviz.

Run riboviz, specifying values for the configuration tokens via environment variables:

$ RIBOVIZ_DATA=$HOME/ribo-data \
  RIBOVIZ_ORGANISMS=$HOME/ribo-organisms \
  RIBOVIZ_SAMPLES=$HOME/ribo-samples \
  nextflow run $HOME/riboviz/prep_riboviz.nf  -ansi-log false -params-file riboviz_env.yaml

Optionally, run integration tests:

$ RIBOVIZ_DATA=$HOME/ribo-data \
  RIBOVIZ_ORGANISMS=$HOME/ribo-organisms \
  RIBOVIZ_SAMPLES=$HOME/ribo-samples \
  pytest -vs $HOME/riboviz/riboviz/test/integration/test_integration.py \
  --expected=$HOME/test-data-2.2 --skip-workflow --config-file riboviz_env.yaml