…ded Parameters for MEGAN. Minscore now computed as percentage.
…mination error. Fixed index-building error. Close #28.
…oining. Fixed Denovo Assembly indexing.
…s file deletion on error. Close #45.
…d MEGAN file task error. Fixed timing scope error. Fixed task reporting error.
… Online link repository. Changed double quotes to single quotes when possible for clarity. Beginnings of support for MEGAN 4.0 (soon to exit beta).
…ated logging. Closes #3. Logging is not only more robust and correct, but is now linked directly with all shell commands executed. Logging information may be added to reports at some point. Provide useful information about data.
…by BLAST+ now supported. Removed comparison feature of contig comparison. The MEGAN comparison feature was found to prevent the ability to change LCA parameters, thus FASTA contigs are joined instead.
type over rides via commandline.
Rewrote the logic to determine if the NT database was installed. Changed all find commands to execute locate if it's installed, but if the file is not found by locate or if locate is not installed, find is run. Reserialization of the configuration files was failing, so I added a task which will automatically be executed at the end of each task list instead. Not fully tested.
v0.27. Added semi-colons to ends of some of shell commands. Included ability to search system for NT database. Added blastInstall to dependency of ntInstall.