thread num not honored and request to not hardcode requirements PATH

[alexweisberg]

Hi,

It seems that there are several places in the code where the user input number of threads is ignored and it just uses 10 or 20 by default.

Additionally, would it be possible to not hardcode the location of the dependencies, such as blast or diamond, and just get them from the PATH/environment variable? This would make it much easier to install as well as incorporate with other tools.

Thanks!