Dave B.

Add datatype definition for AGP assemblies

8

This adds support for the "[A Golden Path](https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/)" 2.0 assembly file format created by NCBI, as requested at the VGP meeting earlier this week. ## How to test the changes?...

Add converter for Kraken to BIOM.

11

Concerns: For the tests to work, the JSON output is prettified. This results in somewhat larger output files.

Use Agg backend when saving images. Add option for UTC times.

2

I did some basic testing of this in OSX, and it seemed to work correctly.

Modernize exception handling for devteam tools

6

Also gets rid of `tool_dependencies.xml` for those tools.

Update cummeRbund to retrieve genes and samples from input metadata.

1

This depends on galaxyproject/galaxy#6302 and should resolve galaxyproject/usegalaxy-playbook#110 and #340