get-bams Get storage directories, use `pattern` to
get-bed Get a BED file for a given Sequencing...
get-count Get count of database instances.
get-data Get file paths for experiments raw data.
get-metadata Retrieve metadata for multiple instances.
get-outdirs Get analyses outdirs, use `pattern` to match...
get-paths Get storage directories, use `pattern` to
get-reference Retrieve reference data from assemblies...
get-results Get analyses results.
import-bedfiles Register targets and baits BED files in a...
import-data Find and import experiments data from many...
import-reference-data Register reference data for assemblies...
import-reference-genome Register an assembly reference genome.
login Login with isabl credentials.
merge-individual-analyses Merge analyses by individual.
merge-project-analyses Merge analyses by project.
patch-results Update the results field of many analyses.
process-finished Process and update finished analyses.
rerun-signals Rerun failed signals.
run-failed-analyses Command to run failed analyses in batch.
run-signals Run any arbitrary signal on analyses or...
run-web-signals Run signals triggered from the frontend.
Some of these commands are only available for the admin user, like:
To manage files and data (See Importing Data):import-data, import-bedfiles, import-reference-data, import-reference-genome
To change permissions of finished analyses: process-finished
To update the linked results of completed analyses: patch-results
Create your custom CLI Commands
You can customize your available commands, by extending the isabl-cli. The following are examples of cases where you want to create commands that execute more than one app at the same time, or create a method for a common metadata query: