CCBR Tools: Utilities for CCBR Bioinformatics Software

New features

• jobby overhaul (#59, @kopardev)
  • Uses saccount to get slurm job information, which should work for any HPC running slurm.
  • Has options --tsv, --json, and --yaml to output the job information in those formats. If not specified, markdown is used.
  • Can accept a snakemake log file, nextflow log file, or a list of slurm job IDs as input.
• module_list is a new utility to list all loaded modules as JSON or retrieve the version of a specific module. (#63, @kopardev)
• ccbr_tools install has new options: (#60, @kelly-sovacool)
  • --type to specify the type of tool to install (e.g. PythonTool, BashTool, Snakemake, or Nextflow).
  • --hpc (e.g. biowulf, frce) to specify the HPC environment for debugging purposes.

Bug fixes

• Fix ccbr_tools install: use relative paths for symlinks within the same directory. (#58, @kelly-sovacool)