[Debian-med-packaging] Bug#1010653: busco: add autopkgtest to check integration with hmmer and prodigal

[Sascha Steinbiss]

Hi all,

>> We might still download one of them at autopkgtest time but I am not sure
>> that's a good idea. Any comments?

BTW datasets are regularly downloaded anyway by the busco tool when 
specifying a lineage on the command line. So if that's the way it's 
usually done with the installed version, then I would suggest to also do 
it like that in the autopkgtest. This way we won't have to distribute 
files with a ND license as Debian, and would also be testing the 
intended mode of use. I wonder why Andrius explicitly asked for the 
`--offline` option which would disable that option. IIRC autopkgtests 
are expected to have Internet available.

However, I noticed that doing something like

$ busco -l euglenozoa_odb10 -i foo.fasta -o out -m genome

already fails with

2023-01-21 16:44:08 INFO:	***** Start a BUSCO v5.4.4 analysis, current 
time: 01/21/2023 16:44:08 *****
2023-01-21 16:44:08 INFO:	Configuring BUSCO with local environment
2023-01-21 16:44:08 INFO:	Mode is genome
2023-01-21 16:44:08 INFO:	Downloading information on latest versions of 
BUSCO data...
2023-01-21 16:44:11 INFO:	Input file is /tmp/foo.fasta
2023-01-21 16:44:11 ERROR:	metaeuk tool cannot be found. Please check 
the 'path' and 'command' parameters provided in the config file or make 
sure the tool is available in your working environment.
2023-01-21 16:44:11 ERROR:	BUSCO analysis failed!
2023-01-21 16:44:11 ERROR:	Check the logs, read the user guide 
(https://busco.ezlab.org/busco_userguide.html), and check the BUSCO 
issue board on https://gitlab.com/ezlab/busco/issues

So it looks like metaeuk is not found -- is this even packaged? Did I do 
something wrong (note: busco 5.4.4 from unstable)?

Thanks
Sascha
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