CCBR Tools

Utilities for CCBR Bioinformatics Software

Installation

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

module load ccbrpipeliner

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

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

Or specify a specific tagged version or branch:

pip install git+https://github.com/CCBR/Tools@v0.1.0

Usage

CLI

ccbr_tools --help

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

  Utilities for CCBR Bioinformatics Software

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

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

Commands:
  cite     Print the citation in the desired format
  version  Print the version of ccbr_tools

All installed tools:
  ccbr_tools
  gb2gtf
  hf
  intersect
  jobby
  jobinfo
  peek

Python

import ccbr_tools.pkg_util
print(ccbr_tools.pkg_util.get_version())

0.1.1-dev

CLI Utilities

Command-line utilities in CCBR Tools.

ccbr_tools
gb2gtf
hf
intersect
jobby
jobinfo
peek

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
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
spooker
which_vpn.sh

Citation

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

Sovacool K., Koparde V., Kuhn S., Tandon M., Huse S. (2024). CCBR Tools: Utilities for CCBR Bioinformatics Software (version v0.1.0). DOI: 10.5281/zenodo.13377166 URL: https://ccbr.github.io/Tools/

Bibtex entry

@misc{YourReferenceHere,
author = {Sovacool, Kelly and Koparde, Vishal and Kuhn, Skyler and Tandon, Mayank and Huse, Susan},
doi = {10.5281/zenodo.13377166},
month = {8},
title = {CCBR Tools: Utilities for CCBR Bioinformatics Software},
url = {https://ccbr.github.io/Tools/},
year = {2024}
}

CCBR / Tools

readme