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Tools development version

  • use major & minor version for docs website subdirectories. (#15, @kelly-sovacool)

Tools 0.1.1

  • fix: don't add extra newline to command stdout/stderr for shell_run() and exec_in_context(). (#10, @kelly-sovacool)
  • minor docuemntation improvements. (#12, @kelly-sovacool)

Tools 0.1.0

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

Tools 0.0.1

This tag marks the repository state from before refactoring it as a python package.