Treffer: 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 ; Please cite CCBR Tools as below