Changelog

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

[0.13.0] - unreleased

Added

• --pipeline-kwargs arguemnt to refgenie build command, which allows you to pass keyword arguments to the pypiper pipeline.

[0.12.1] - 2021-11-04

Fixed

• A bug with setuptools no longer allowing use_2to3.

[0.12.0] - 2021-06-28

Added

• MapReduce framework support in refgenie build that supports automating asset builds at scale (--map and --reduce options)
• an option to automatically pull parent assets when building a derived asset (--pull-parents option in refgenie build)

Fixed

• misleading exit codes in refgenie build; #258

[0.11.0] - 2021-04-27

Added

• remote commands, which work without genome config file:
  • refgenie seekr
  • refgenie populater
  • refgenie listr
• refgenie populate command for refgenie registry paths populating with local paths
• --flag-meanings argument to refgenie compare command

[0.10.0] - 2021-03-11

Version 0.10.0 requires an upgrade to the configuration file and asset structure. Please refer to the upgrade tutorial for instructions on how to migrate your config upon upgrade to 0.10.0.

Changed

• instead of using human-readable names as genome identifiers refgenie uses sequence-derived digests in the config
• asset data moved to data directory
• asset files are now named after genome digests
• refgenieserver API v3 is now used for remote assets retrieval
• improved visual interface in list, listr and pull subcommands

Added

• data and alias directories in genome directory that are used to store asset and aliases data, respectively
• refgenie alias command for genome aliases management
• refgenie upgrade command for config format upgrades
• refgenie compare command for genome compatibility determination

[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