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CHANGELOG.md

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Tools development version

  • new commands:
    • ccbr_tools send-email for sending emails from the command line. (#26, @kelly-sovacool)
      • With new helper function: send_email.send_email_msg().
      • Works when run from biowulf.
    • ccbr_tools quarto-add to add quarto extensions from this package. (#30, @kelly-sovacool)
      • Includes new format fnl for our documentation websites.
  • new functions for creating a contributors page for documentation websites: github.print_contributor_images(). (#27, @kelly-sovacool)
  • new script from CCBR/TaskManagement: github_milestones.sh. (#29, @kelly-sovacool)
  • documentation improvements:
    • fix docstrings rendering -- use Google style. (#25, @kelly-sovacool)
    • overhaul navigation structure of docs website. (#28, @kelly-sovacool)
    • style the website to follow FNL branding guidelines. (#30, @kelly-sovacool)
    • miscellaneous minor improvements. (#32, @kelly-sovacool)
  • bug fixes:
    • include data files in package installation for homologfinder. (#31, @kelly-sovacool)

Tools 0.1.3

  • fix shared SIF cache directory spelling for biowulf. (#23, @kelly-sovacool)

Tools 0.1.2

  • use major & minor version for docs website subdirectories. (#15, @kelly-sovacool)
  • fig bug where nextflow.run() did not import the correct HPC modules. (#20, @kelly-sovacool)
  • fix bug in _get_file_mtime(). (#21, @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/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.