Fixed dockerfile

Add install of headless default JRE to Dockerfile (fixes #140).

Docker image dependency check and tests fixed

Docker image fix

• Locales were not properly set, breaks Circlator dependency checks (nucmer) when run in Singularity
• Test files were not readable in Singularity

AMOS and openpyxl dependency fixes

AMOS install to support minimus2 pipeline in docker image
h/t Yuri Bendaña (ybendana) for working AMOS install -- see PR #151

openpyxl needs a downgrade to 2.6.4 to keep compatibility with circlator

Fixed dockerfile

• docker build includes 2 extra debian packages
• docker build now builds from local repo (used to clone from github for every build, which was rather unconventional and made it harder to build with local changes)

Prevent infinite recursion

Merge pull request #126 from andrewjpage/infinite_recursion

failsafe to prevent infinite recursion

Improved version string handling for external dependancies

Plus some tests

Fix nucmer version

Merge pull request #120 from ssjunnebo/master

version bump

Version 1.5.1

Bug fixes (thanks @NicolaDM for reporting):

• getting Canu version 1.5
• parsing canu output graph file

Version 1.5.0

• Option to use Canu instead of SPAdes for reassemblies. Thanks to @NicolaDM for contributions.

Version 1.4.1

Fixes a bug where --assemble_not_only_assembler caused it to crash (issue #80).