phylociraptor v0.9.9

Changes since last release:
683f9cb bump version to 0.9.9
516648b Add new util function manage-jobs to list and cancel submitted hpc jobs
e14e15f Correct error in cluster-config for SGE file
5ca510e Remove several old config files
669781a Modify cluster log path for test case cluster config files
b016a4d Fix bug in serial-local transition. Better reporting of downloaded singularity containers: Now warning will only displayed if container is actually downloaded
58698c4 Rename serial to local for -t to omit confusion.
2ded668 Change default location of cluster logfiles for better organization of all logfiles
ee31e40 Add better logging and organization of log files
94e2b53 Add missing info to util modify-busco
3979ee2 Add initial logging functionality to phylociraptor script
0d96b6a fix unusual amino acid letters to prevent alicut errors
f87add5 apply exclude filter in filter-orthology
5d95fdc Several small fixes and tweaks
a8e8770 Add missing rulenames to cluster config file templates
7187ea0 make rename assemblies use relative paths or copy if files are 'outside'