DarkHorse-2.0_rev09

Fixes an installation problem specific to Oracle-community MySQL, the current default MySQL server software for macOSX. The macOSX problem was caused by an Oracle-specific reserved keyword ("rank"), which conflicts with a field name in the nodes table of the NCBI-Genbank taxonomy-db. No corresponding problem exists for MariaDB (the default MySQL program for Linux), which does not use this keyword. The issue was resolved by modifying sql statement formats in the accessory program recursive_taxonomy_taxid.pl. For user reference, an example of a successful installation logfile was added to the "templates" directory.

DarkHorse-2.0_rev08

Minor update. Added parameter settings for min_lineage_terms and min_align_coverage to logfile output, fixed compatibility problem in load_taxonomy_nodes.pl when using strict MYSQL program settings, and modified getseq_multiple_nr.pl for perl path consistency with other subscripts.

DarkHorse-2.0_rev07

• Fixed bug in blast match filtering for minimum alignment coverage (filters were not being executed due to unexpected extra space characters in match id numbers in Diamond blast output).
• All optional command-line input parameters now take precedence over default values listed in config file, facilitating multiple optimization runs for specific data sets (e.g. empirically increasing or decreasing stringency of potential database ortholog match criteria).

DarkHorse-2.0_rev06

• Updated taxonomy database loading syntax for compatibility with MySQL version 5.7.
• Reduced default minimum number of taxonomy terms from 3 to 2, to accommodate new candidate bacterial phyla in NCBI taxonomy database.

DarkHorse-2.0_rev05

Fixed bug in installation script recursive_taxonomy_taxid.pl that included "root" in lineage for unclassified taxa. Note: program permissions may need to be re-set as executable after decompressing the downloaded files, e.g.

tar -xzvf DarkHorse-2.0_rev05.tar.gz
chmod -R 755 DarkHorse-2.0_rev05

DarkHorse-2.0_rev04

Modified installer to clarify mandatory user inputs. Reduced stringency of default parameters in config_template. Added documentation for accessory script enabling automated keyword generation.

DarkHorse-2.0

Initial release of DarkHorse version 2