Torsten Seemann

I am now unable to get `cpanm Bio::Perl` to install on OS X, whereas Linux works fine. The issue is the `Bio::DB::` stuff as @cjfields had in https://github.com/bioperl/bioperl-live/issues/264 I am...

I'm pure brew AFAIK. I use `cpanm` for everything, from brew also. ``` brew info perl perl: stable 5.26.1 (bottled), HEAD Highly capable, feature-rich programming language https://www.perl.org/ /usr/local/Cellar/perl/5.26.1 (3,009 files,...

@cjfields sorry but all the macs i have access to are High Sierra now.

@cmdcolin I am not using macperl. I use `brew install perl cpan-minus` and use `cpanm` to install all in the brew hierarchy. so it's something else?

Will it support 4k screens? 📺

@EisenRa giving BEAST all the invariant sites will slow it down unnecessarily. i think the right approach is to include the constant site numbers in the BEAST XML file. This...

if you wanted to mask the recombinant regions that gubbins (or clonalframeml) computer then yes passing them to `snippy-core --mask FILE.BED` is the best solution. you should never mask recombination...

You can't run gubbins on a single genome - it needs a full genome alignment of all your isolates. It has to be done after the snippy-core step. You can...

Yep, it's good if you can get it to work when you have > 10 contigs.

I suggest using https://docs.python.org/3/library/tempfile.html which will automatically clean up for you at end of process. I note that assemblerflow manually attempts to clean it up with `rm -r blah/temp` but...