Tools development version

  • Fixes for ccbr_tools install: (#98, @kelly-sovacool)
    • Correct installation method for spacesavers2.
    • Change symlink permissions so group members can edit them.

Tools 0.4.3

  • Add standalone script to retrieve HPC cluster name. (#93, @kopardev)
  • module_list now retrieves the full module version. (#93, @kopardev)

Tools 0.4.2

  • Fix ccbr_tools install: add group write permissions after installation. (#89, @kelly-sovacool)
  • Updates to nextflow.run(): (#90, @kelly-sovacool)
    • Allow pipelines to pass in module versions.
      • This is needed for the next version of champagne which will use nextflow v25 for the new output directive, while other pipelines will continue to use the default nextflow module version.
    • Ensure nextflow.run() stops if the nextflow preview errors out.

Tools 0.4.1

  • Breaking change: Spooker now takes named options rather than positional arguments. (#85, @kelly-sovacool)
  • jobby now omits log columns when the format is markdown, even if --outerr is used. (#86, @kopardev)
  • Minor documentation improvements. (#81, @kelly-sovacool)

Tools 0.4.0

New features

  • jobby overhaul (#59, #75, @kopardev)
    • Uses saccount to get slurm job information, which should work for any HPC running slurm.
    • Has options --tsv, --json, and --yaml to output the job information in those formats. If not specified, markdown is used.
    • Can accept a snakemake log file, nextflow log file, or a list of slurm job IDs as input.
    • Can include the job stdout/stderr log files (--outerr) for only failed jobs or all jobs (--include-completed). (#71, @kelly-sovacool)
  • module_list is a new utility to list all loaded modules as JSON or retrieve the version of a specific module. (#63, @kopardev)
  • ccbr_tools install has new options: (#60, @kelly-sovacool)
    • --type to specify the type of tool to install (e.g. PythonTool, BashTool, Snakemake, or Nextflow).
    • --hpc (e.g. biowulf, frce) to specify the HPC environment for debugging purposes.
  • spooker updates:
    • Now accepts the path to the pipeline CLI as an optional argument. (#69, @kelly-sovacool)
    • Now bundles all pipeline information into a single gzipped JSON file. (#71, @kelly-sovacool)
      • A tar archive is no longer created, as only one file is now needed.
      • The tree & jobby information are included as strings in the JSON file.
  • New shared conda environment on biowulf: py3.11-8 for ccbrpipeliner/8. (#79, @kelly-sovacool)

Bug fixes

  • Fix ccbr_tools install: use relative paths for symlinks within the same directory. (#58, @kelly-sovacool)

Tools 0.3.2

  • Fix ccbr_tools install: use the full path to the conda env on biowulf. (#64, @kelly-sovacool)

Tools 0.3.1

  • Bug fixes in ccbr_tools install:
    • ccbr_tools & ccbr_actions were using incorrect repo names. (#53, @kelly-sovacool)
    • absolute paths were not being used for the symlinks. (#55, @kelly-sovacool)
  • Minor documentation improvements. (#54, @kelly-sovacool)

Tools 0.3.0

  • Allow relaxed version with only major and minor components in match_semver() with strict_semver=False. (#49, @kelly-sovacool)
  • Remove args and add repo parameter to get_latest_release_tag() and get_latest_release_hash(). (#51, @kelly-sovacool)

Tools 0.2.4

  • Fix ccbr_tools.pipeline.nextflow.run: (#46, @kelly-sovacool)
    • make sure preview loads necessary modules.
    • improve stack trace when nextflow command fails.
  • New theme templates based on the FNL branding guide: (#47, @kelly-sovacool)
    • mkdocs-fnl for websites built with mkdocs material.
    • pkgdown-fnl for R package websites built with pkgdown.
  • Create helper to install software on supported HPCs.
    • usage: ccbr_tools install TOOL_NAME VERSION_TAG

Tools 0.2.3

  • Output ccbrpipeliner module version in spooker metadata. (#43, @kelly-sovacool)
  • Spooker now correctly outputs metadata as a yaml file. (#43, @kelly-sovacool)
  • Improvements to ccbr_tools.pipeline.nextflow.run: (#44, @kelly-sovacool)
    • Use -resume by default and turn it off with --forceall.
    • Use --output option.
    • Run -preview before launching the pipeline with slurm.
    • When running on biowulf, try adding spooker to the PATH if it’s not available.

Tools 0.2.2

  • Fix bug where spooker failed when more than 2 arguments were passed. (#41, @kelly-sovacool)

Tools 0.2.1

  • Spooker update: accept pipeline version as an optional third positional argument. (#39, @kelly-sovacool)
  • Bump cffconvert version for compatibility with nf-schema. (#38, @kelly-sovacool)

Tools 0.2.0

  • 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 0.1.4

  • fix copy location for spook. (@kopardev)

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.