GenHub version 0.4.0

Changed

• The genhub-build.py script is now fidibus, and the CLI was updated.
• Pdom, Pcan, and Dqua now default to RefSeq genomes, with Toth Lab and CRG genomes available under labels Pdtl, Pccr, and Dqcr.

Fixed

• The cluster build task now uses -M 0 by default.
• The Registry class was simplified.

Added

• The build script (now fidibus) now has support for custom genomes.
• Sequence IDs are now reported for iLocus and miLocus tables.
• New script for creating a piLocus summary table.
• Recipes for chick pea, cabbage, and soybean.
• Recipes for another mosquito (Aedes aegypti) and a spider mite (non-insect arthropod).
• A --shuffled option to several scripts for reading from *iloci.shuffled.tsv, and improved access from the GenomeDB class.

GenHub version 0.3.7

Fixed

• Correctly included missing script in setup.py.

GenHub version 0.3.6

Added

• New recipe for cotton.
• New recipe for Daphnia pulex.
• New script for creating an iLocus summary table.

GenHub version 0.3.5

Fixed

• Updated test data files to compensate for corrections to LocusPocus' reporting of iLocus type.

GenHub version 0.3.4

Added

• Added seqfilter to RefSeq module and .yaml configs.

Fixed

• Used new seqfilter mechanism to eliminate redundant patch and variant data from human and mouse genomes.
• Updated rice recipe following an update to the corresponding RefSeq entry.

GenHub version 0.3.3

Fixed

• Filled out partial implementation of --delta option for the build script.

GenHub version 0.3.2

Fixed

• Removed gene model with overlapping exons causing processing issues in C. reinhardtii.

GenHub version 0.3.1

Fixed

• Removed unnecessary Fragment column from .iloci.tsv table. Redundant with LocusClass=fiLocus.
• Removed outdated code for computing LocusClass.
• Fixed feature for specifying iLocus label format.

GenHub version 0.3.0

Added

• Integration with codecov.io.
• Lots of genome recipes
  • Anopheles gambiae
  • Homo sapiens
  • Theobroma cacao
  • some version-specific recipes
    • TAIR6
    • Apis mellifera assembly 2.0 / OGS 1.0
    • Apis mellifera assembly 4.5 / OGS 3.2
  • 9 species of green algae
• Implemented the cleanup and cluster tasks for the main build script.

Changed

• Unit test fixtures to account for AEGeAn's improved reporting of iLocus types.
• Protein checksum for Xenopus tropicals, which was recently updated to drop the Silurana designation.

GenHub version 0.2.1

Fixed

• versioneer issue with MANIFEST