KronaTools-2.7

Features

• Charts now take full advantage of high resolution (e.g. Retina) displays.
• updateTaxonomy.sh has been improved for installations without internet
  connectivity.
  • --local has been divided into --only-fetch and --only-build, so
    data dumps can be downloaded automatically before transferring.
  • Custom taxonomy directories can now be relative paths.
  • A new --preserve option prevents data dumps from being removed after
    building, if needed for other uses.
  • Data dumps can be unzipped/untarred.
  • Updating the taxonomy ID lookup database (now by accessions), has been
    split out to updateAccessions.sh, which cuts most of the running time from
    updateTaxonomy.sh when lookups are not needed.
• New taxonomy convenience scripts
  • ktGetTaxInfo lists depth, parent, rank, and name for taxonomy IDs, or
    can directly take accessions, if the database has been installed with
    updateAccessions.sh.
  • ktGetLCA returns the lowest common ancestor for groups of taxonomy IDs,
    or can directly take accessions, if the database has been installed with
    updateAccessions.sh.

Fixes

• ktImportKrona will no longer fail if a chart's supplemental files are not
  available.
• ktImportTaxonomy no longer erroneously creates supplemental file folders
  for large imports without query IDs.

Changes

• GI lookups have been replaced with accession lookups due to the impending
  retirement of GIs by NCBI.
  • ktGetTaxIDFromGI is now ktGetTaxIDFromAcc.
• ktGetLibPath, which caused problems with multiple KronaTools installations,
  is no longer used by official scripts, which now always use relative paths to
  find their appropriate libraries and data. The command is still available for
  third-party inclusion of the KronaTools library .
• Warnings and errors are now directed to STDERR instead of STDOUT.
• The "Unassigned" (gray) section of the current chart view is now "other"
  for clarification.