Skip to contents

Changelog

Source: NEWS.md

BLASTr 0.1.7

Release Date: 2025-11-03

Development Changelog: dev

Added

  • New retry_times argument in parallel_blast() to specify the number of retries for failed BLAST jobs. Defaults to 10 times.

  • New verbose = "progress" in parallel_blast() to show a progress bar for the BLAST jobs.

  • New get_blastr_cache() for printing the directory used as cache for BLASTr.

Changed

  • parallel_blast() will not throw errors immediately when a BLAST job fails. Instead, it will log the error and continue with the remaining jobs.

  • parallel_blast() output has two new columns:

    • exit_code: The exit code of the BLAST command.
    • stderr: The standard error output from the BLAST command.

  • parallel_blast() will automatically retry failed BLAST jobs up to 10 times before giving up.

  • Arguments out_file and out_RDS in parallel_blast() are removed.

  • Argument asvs is renamed to query_seqs in parallel_blast().

BLASTr 0.1.6

Release Date: 2025-10-28

Development Changelog: 0.1.6

Fixed

  • Fix hard coded num_threads = 1L in parallel_blast(). parallel_blast() now correctly uses the user provided num_threads argument.

  • Fix parallel functions not using the the custom compute profile. purrr::map do not have an argument for specifying the mirai .compute argument correctly. Now all parallel functions use the “default” mirai compute profile .compute = NULL.

  • Fix get_tax_by_taxID() when multiple tax IDs are provided.

  • Fix parse_fasta() concatenate lines for multiline FASTA.

BLASTr 0.1.5

Release Date: 2025-08-27

Development Changelog: 0.1.5

Added

  • New parallel framework based on native purrr functions, using mirai and carrier in the background.

  • New make_blast_db() function to create custom BLAST databases.

Changed

  • Internal entrez-direct version bump to 24.0.

  • The internal environments used by BLASTr have been renamed to blastr-blast-env and blastr-entrez-env.

  • Remove of the furrr based functions in favor of the new purrr native parallel.

  • All options() based parameters have been removed in favor of explicit arguments in the functions.

BLASTr 0.1.4

Changed

  • All functions have better defaults and less mandatory arguments.

Fixed

  • Fix progress bars when parallel processing is used.

BLASTr 0.1.3

Added

  • Refactor handling of internal errors.

  • shell_exec is not available anymore.

BLASTr 0.1.2

Added

  • New install_dependencies() automatically create environments.

  • Initial support for condathis for managing dependency installation.