Changelog

This project adheres to Semantic Versioning and Keep a Changelog format.

[0.7.3] - unreleased

Changed

  • in refgenie build command arguments naming scheme: --{input_name} <path> to --files {input_name}=<path>
  • -r/--requirements in refgenie build command to -q/--requirements
  • recipe format: requirements (both assets and inputs) are lists of dicts rather that lists of strings

Added

  • refgenie id command for asset digest retrieval
  • cross-namespace asset relationships support
  • --assets argument in refgenie build command to provide parent assets, if required
  • -r/--recipe in refgenie build command argument to provide the recipe for the build

Removed

  • -t/--tag in refgenie build. Use more flexible --assets instead.

[0.7.2] - 2019-11-06

Added

  • dbsnp recipe
  • distribute the license file with the package

[0.7.1] - 2019-10-29

Changed

  • --genome-server can now be called multiple times to add additional refgenieservers
  • listr will check each available refgenieserver and display assets
  • pull will check each available refgenieserver and take the first matching asset found

Added

  • possibility to list multiple selected genomes in refgenie list/listr -g

[0.7.0] - 2019-10-21

Added

  • import_igenome command line tool for iGenomes integration with Refgenie
  • --genome/tag-description arguments to the refgenie build command
  • -r/--requirements argument to the refgenie build command recipe requirements to display required inputs and required assets for a particular recipe
  • config manipulation support in multi-user contexts, it's racefree, uses file locks
  • dbNSFP asset recipe
  • assets tagging
  • refgenie tag command that assigns a tag to an assets (re-tags it)
  • refgenie getseq command that retrieves sequence ranges from a genome
  • seek_keys, which provide control over files within an asset
  • asset_digests, which are calculated after asset building and used to assure asset provenance
  • asset relationships recording (asset_children, asset_parents fields)

Changed

  • assets can be referred to by registry paths: genome/asset.seek_key:tag
  • config v0.3 is required
  • refgenie pull uses refgenieserver API v2

[0.6.0] - 2019-08-05

Added

  • list and listr subcommand results can be restricted to a specific genome with -g/--genome options
  • remove subcommand will remove an asset from disk and config
  • Added recipes for new assets: ensembl_gtf and feat_annotation
  • build now populates the asset_description field in the config with corresponding value from the recipe

Changed

  • changed some asset locations; tss_annotation is now named refgene_tss or ensembl_tss and is built by the refgene_anno or ensembl_gtf assets. Renamed gene_anno to refgene_anno.

[0.5.0] - 2019-07-11

Changed

  • refgenie build uses dict-like recipes for build instructions
  • Major genome configuration file format changes

    • Added config_version entry
    • Added assets section in genomes section
  • recipes can now include container images

Added

  • genomes can have attributes, like description
  • Added recipes for new assets salmon, bwa, star, gene_anno, and tss_annotation.

[0.4.4] - 2019-07-01

Added

  • add subcommand

[0.4.3] - 2019-06-21

Changed

  • Build process now builds individual assets

[0.4.2] - 2019-06-18

Added

  • seek subcommand

Changed

  • Require config file arg for init.

Fixed

  • Pick up env var for init config.

[0.4.1] -- 2019-06-14

Fixed

  • Use newer yacman and regain init functionality.

[0.4.0] -- 2019-06-14

Added

  • Added new commands init, pull, list and listr
  • Added connectivity option with remote data sources

[0.3.2] -- 2019-05-14

Fixed

  • Fixed a bug with packaging

[0.3.0] -- 2019-05-10

Added

  • Implemented installable CLI
  • Packaged for release on PyPI
  • Wrote comprehensive docs

Fixed

  • Fixed naming of .fq.gz files

[0.2.0] -- 2017-03-08

Added

  • Transition release as a functional script

[0.1.0] -- 2016-11-11

  • Project started