CCBR Tools: Utilities for CCBR Bioinformatics Software

The Tools repository is now restructured as a Python package. All previous python scripts which included command line utilities have been moved to src/, and all other scripts have been moved to scripts/. In both cases, they are available in the path when the package is installed.

Functions which were part of both XAVIER and RENEE are available for re-use in other bioinformatics pipelines for tasks such as determining the HPC environment, retrieving available genome annotations, and printing citation and version information. Explore the ccbr_tools reference documentation for more information: https://ccbr.github.io/Tools/latest/reference/

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

Full Changelog: https://github.com/CCBR/Tools/compare/v0.0.1...v0.1.0