Dockerfile dependency updates for scripts

[nathanweeks]

Fix #169 , including additional dependencies:

• diamond-aligner (recommended over blastp I assume?) for aa2nonred.pl
• libyaml-perl for yaml2gff.1.4.pl
• libdbd-mysql-perl for autoAug.pl (though note PASA also supports SQLite)
• python3-biopython for fix_in_frame_stop_codon_genes.py and getAnnoFastaFromJoingenes.py (installed using --no-install-recommends to avoid installing ncbi-blast+; if it's desired that still be installed as an alternative to diamond for aa2nonred.pl, just remove that option)
• cdbfasta for fix_in_frame_stop_codon_genes.py

Also, this PR addresses a syntax issue in extractAnno.py revealed by Python 3.8.5:

root@aaed5cebd134:~/augustus/scripts# python3 --version
Python 3.8.5
root@aaed5cebd134:~/augustus/scripts# ./extractAnno.py -h
./extractAnno.py:37: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  split = [x for x in line.split("\t") if x is not ""] 
./extractAnno.py:61: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  split = [x for x in line.split("\t") if x is not ""] 
usage: extractAnno.py [-h] [-c CHUNKS [CHUNKS ...]]

(see https://adamj.eu/tech/2020/01/21/why-does-python-3-8-syntaxwarning-for-is-literal/ for a description of this warning)

Finally, it's handy if the scripts directory is in the PATH (per the Augustus Install locally directions). This PR adds the scripts/ directory to PATH, and adds the execute bit to several scripts that lacked it.

[MarioStanke]

Thanks, Nathan.
Yes, diamond is recommended over blastp due to speed.
Thanks for adding the dependencies, and the other fixes.