Circlator

Removed a few false-positive dnaA genes from the default set used by fixstart.

Add full paths to binaries when running progcheck: see issue 36.

- get_dnaa can take a uniprot search term so any genes can be downloaded, instead of just dnaa.
- when running "circlator all...", writes a file 00.info.txt that has how circlator was run, the version of circlator, and versions of all the dependencies.

- bug fix: stop trying to run spades with python3.4
- added travisCI

- new task progcheck, which checks that Circlator can find the dependencies OK, and also that the versions are high enough
- new task get_dnaa. which generates a fasta file of dnaA genes, downloaded from uniprot.
- default set of dnaA genes now has 2,691 genes, instead of the old one that had <200 genes. Generated using new task get_dnaa
- default minimum % identity needed for a match to a dnaA gene dropped from 80% to 70%. This is now a parameter that the user can change

Bug fix to stop crashing when --ignore not used when running circlator fixstart