Will Trimble

João, can you prepare subsets of the data files (perhaps 20 lines of all of the relevant fastqs?) and the sample mapping file that will produce the bad output? (Short,...

Examine the output of diff tmp/multx.t.dBy4q/test3.out out/multx/test3.out I suspect it is a completely harmless sign difference in the standard deviation of join length calculation.

I think this is a problem with pip. `authors` has the `str` type, which is the right type in python3, but pip can't handle it.

FailToUnderstandError: Do you want another issue, to separate move vs. patch, or do you want me to clean up the commits here?

The automatic build/testing doesn't find scripts that are in sandbox, so the tests I added failed; i thought I had to move the scripts (or the testing would fail horribly)...

The syntax for specifying the authentication token has changed. auth.MGRAST(file="~/Downloads/MGRastAuth.txt") will do what you want.

You have a version of matR that is too old. Reinstall 0.9.1 from CRAN or use the instructions at https://github.com/MG-RAST/matR sessionInfo(matR) other attached packages: [1] matR_0.9

The source is here: https://github.com/MG-RAST/MGRASTer/blob/master/R/source.R So the auth function requires MGRASTer 0.9.1, which isn't in CRAN at the moment. Sorry to have inconvenienced you with unclearly-versioned dependencies.