CCBR Tools 🛠️

Utilities for CCBR Bioinformatics Software

View the website for more detailed documentation: https://CCBR.github.io/Tools

Installation

On biowulf you can access the latest release of ccbr_tools by loading the ccbrpipeliner module:

sh module load ccbrpipeliner

Outside of biowulf, you can install the package with pip:

sh pip install git+https://github.com/CCBR/Tools

Or specify any tagged version or branch:

sh pip install git+https://github.com/CCBR/Tools@v0.2.4

Basic usage

CLI

sh ccbr_tools --help

Usage: ccbr_tools [OPTIONS] COMMAND [ARGS]...

  Utilities for CCBR Bioinformatics Software

  For more options, run: ccbr_tools [command] --help

  https://ccbr.github.io/Tools/

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

Commands:
  send-email  Send an email (works on biowulf)
  quarto-add  Add a quarto extension
  install     Install a specific version of a CCBR software package,...
  cite        Print the citation in the desired format
  version     Print the version of ccbr_tools

All installed tools:
  ccbr_tools
  gb2gtf
  get_hpcname
  hf
  intersect
  jobby
  jobinfo
  module_list
  peek
  spooker

Python

python import ccbr_tools.shell print(ccbr_tools.shell.shell_run('echo "Hello, world!"'))

Hello, world!

python import ccbr_tools.versions version = ccbr_tools.versions.match_semver('0.2.3') version.groupdict()

{'major': '0',
 'minor': '2',
 'patch': '3',
 'prerelease': None,
 'buildmetadata': None}

View the API reference for more information: https://ccbr.github.io/Tools/reference/

CLI Utilities

Command-line utilities in CCBR Tools.

• ccbr_tools
• gb2gtf
• get_hpcname
• hf
• intersect
• jobby
• jobinfo
• module_list
• peek
• spooker

Run a command with --help to learn how to use it.

External Scripts

Additional standalone scripts for various common tasks in scripts/ are added to the path when this package is installed. They are less robust than the CLI Utilities included in the package and do not have any unit tests.

• add_gene_name_to_count_matrix.R
• aggregate_data_tables.R
• argparse.bash
• cancel_snakemake_jobs.sh
• create_hpc_link.sh
• extract_value_from_json.py
• extract_value_from_yaml.py
• filter_bam_by_readids.py
• filter_fastq_by_readids_highmem.py
• filter_fastq_by_readids_highmem_pe.py
• gather_cluster_stats.sh
• gather_cluster_stats_biowulf.sh
• get_buyin_partition_list.bash
• get_slurm_file_with_error.sh
• github_milestones.sh
• gsea_preranked.sh
• karyoploter.R
• make_labels_for_pipeliner.sh
• rawcounts2normalizedcounts_DESeq2.R
• rawcounts2normalizedcounts_limmavoom.R
• run_jobby_on_nextflow_log
• run_jobby_on_nextflow_log_full_format
• run_jobby_on_snakemake_log
• run_jobby_on_snakemake_log_full_format
• which_vpn.sh

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

Citation

Please cite this software if you use it in a publication:

Sovacool K., Koparde V., Kuhn S., Tandon M., and Huse S. (2025). CCBR Tools: Utilities for CCBR Bioinformatics Software (version v0.4.3). DOI: 10.5281/zenodo.13377166 URL: https://ccbr.github.io/Tools/

Bibtex entry

bibtex @misc{YourReferenceHere, author = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan}, doi = {10.5281/zenodo.13377166}, month = {6}, title = {CCBR Tools: Utilities for CCBR Bioinformatics Software}, url = {https://ccbr.github.io/Tools/}, year = {2025} }