Changelog

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

[0.9.3] - 2020-07-29

Changed

  • short option string for --no-overwrite from -n to -o

Added

  • option to handle large asset archives pulling from the CLI (-l/--no-large flag)
  • option to set the maximum archive size to pull with no confirmation required (--size-cutoff argument)
  • -s/--seek-keys argument to refgenie add to specify seek keys for added assets

Fixed

  • refgenie add issues -- added assets are no longer imported to the genome_folder; #180

[0.9.2] - 2020-07-01

Changed

  • in refgenie build reduced the config file locking time to prevent problems in multi-build context
  • dropped Python 2 support

Added

  • parametrized kmer in salmon recipes
  • support for all genome configuration file parameter values initialization in refgenie init

[0.9.1] - 2020-05-01

Added

  • added option (-f/--force) to confirm assets overwriting upfront in refgenie add add refgenie pull

Changed

  • fixed bug in hisat2_index that pointed to the parent folder. The seek key now points to the folder/{genome}, as expected by the tool
  • fixed bug in bwa_index that pointed to the parent folder. The seek key now points to the folder/{genome}.fa, as expected by the tool

[0.9.0] - 2020-03-17

Changed

  • fixed a bug in bowtie2_index recipe that pointed to the parent folder. The seek key now points to the folder/{genome}, as expected by bowtie2
  • in refgenie seek file existence check is not performed by default

Added

  • possibility to execute library module as a script: python -m refgenie ...
  • support for repeated recipe inputs on CLI (arguments: --files, --assets and --params)
  • a possibility to perform file existence check (-e/--check-exists) in refgenie seek

[0.8.2] - 2020-01-08

Fixed

  • SyntaxError in Python 2.7; #155

[0.8.1] - 2019-12-13

Fixed

  • salmon_partial_sa_index recipe

Changed

  • refgenie remove removes the asset relatives links
  • refgenie init uses initialize_config_file method from refgenconf
  • default input assets for salmon_sa_index and salmon_partial_sa_index recipes to transcriptomes within the namespace

Added

  • threads parameter to the following recipes: dbnsfp, salmon_index, star_index

Removed

  • documentation regarding -r/--recipe option in refgenie build. It will be removed in the future

[0.8.0] - 2019-12-06

Changed

  • 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
  • refgenie list displays current server subscriptions

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
  • subscribe and unsubscribe subcommands to enable server list manipulation in the config file (genome_servers entry in the refgenie configuration file)
  • new recipes:
    • salmon_sa_index
    • salmon_partial_sa_index
    • suffixerator_index
    • tallymer_index

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