Release 0.7.0

[0.7.0] - 2019-11-18

Added

• Direct downloading from url through url provider.
• Added --force flag. Files will no longer be overwritten by default.
• Provider specific options:
  • --ensembl-version: specify release version.
  • --ensembl-toplevel: by default, genomepy install will search for primary assemblies.
    This flag will only download toplevel assemblies.
• Added STAR index plugin

Changed

• Providers are now case-insensitive.
• Extended testing.
• Increased minimal Python version to 3.6.
• Removed gaps from plugins, added gaps to core functionality.

Fixed

• bugfix: NCBI will show all versions of an assembly (will no longer filter on BioSample ID, instead filters on asm_name).
• fix: gaps file will be generated when needed.

Release 0.6.1

[0.6.1] - 2019-10-10

Bugfix release

Fixed

• Fixed bug with get_track_type().

Release 0.6.0.

Added

• Support for storing bzgip-compressed genomes (#41).

Changed

• Removed support for Python 2 (2020 is close!).

Fixed

• Ensembl annotation for non-vertebrate genomes should work again.
• Fixed bug where a deleted or empty config file would result in an error.

Release 0.5.5

[0.5.5] - 2019-03-19

Added

• Plugin for downloading genome blacklists (from Kundaje lab).

Fixed

• Fix for new Ensembl REST API and FTP layout.
• Genomes from Ensembl with a space in their name can be downloaded.
• Plugin imports use relative parts to prevent conflicts with other imports.

Release 0.5.4

Added

• Downloading annotation from NCBI now implemented.
• Genbank assemblies at NCBI can be searched and downloaded

Fixed

• Fixed #23.
• Fixed #26.
• Fixed Ensembl downloads (#30)
• Fixed FTP tests for CI

Release 0.5.2

• Fixed genome_dir argument to genomepy install
• Fixed msgpack dependency
• Fixed issue with config generate where config directory does note exist.

Release 0.5.1

Release notes:

• Fixed installation issue with msgpack

Release 0.5.0

Release notes:

• Added support for indexing genomes (bwa, bowtie2, gmap, hisat2, minimap2)
• Added configuration management
• Switched tests to py.test

Release 0.4.0

Changes:

• Optionally download annotation in BED and GTF format.
• Create BED file with gaps.

Version 0.3.1

Bugfix release. Changes:

• Added requests dependency
• Removed dependency on xdg, as it didn't support OSX
• Fixed string decoding bug