Solosis

CLI tool including common computational utilities for single-cell sequencing data analysis used by the Haniffa Lab. This tool is made to work with farm22.

Documentation

• Setup
• API
• Examples

Quick-start

3 initial commands to start using solosis.

1. To use Solosis from the Wellcome Sanger Institute, add the module path.

Input

module use append /software/cellgen/team298/shared/modulefiles

2. Then load the Solosis module.

Input

module load solosis

Expected Output

** INFO: 'Welcome to Solosis, Module loaded'
** INFO: 'Type solosis-cli to get started'

Loading solosis/0.3.0
   Loading requirement: cellgen/conda /software/modules/ISG/experimental/irods/4.2.11 cellgen/irods

3. Execute the main solosis command to view available tools & commands.

Input

solosis-cli

Expected Output

Usage: solosis-cli [OPTIONS] COMMAND [ARGS]...

 Command line utility for the Cellular Genetics programme at the Wellcome
 Sanger Institute

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

Commands:

 alignment   Commands for running alignment tools.
 filesystem  Commands for file and directory operations.
 irods       Commands for working with iRODS.
 ncl-bsu     Commands for Newcastle University BSU.
 sc-rna      Commands for single-cell RNA-seq workflows.