Question: Hello fellow Biostars,

while reading the answers of you folks to difficult questions in this forum, I figured that, if anyone in the internet, only you can save a desperate man like me, who is new to bioinformatics, with your impressive knowledge and experience! I am looking forward to you answers and do not think that you guys will be intimidated by a post that is a bit longer!

So I recently installed BUSCO, and while the test busco run yields the exact log that I am supposed to yield and the analysis do run without any errors, I still do not know whether I have made any mistakes. I do not want to discard all of my analysis in the end because I made a decisive mistake in the beginning, Therefore I wanted to ask you guys a couple of questions. Specifically there are a few tips in the user guide that I chose to ignore, because I thought that I would crush my entire seemingly working installation, if I tried to implement them in the wrong manner (https://busco.ezlab.org/busco_userguide.html#mandatory-arguments).

Info: I am trying to examine the quality of genome assemblies of many plants and algae. I chose the installation via anaconda.

1. At first I wanted to use metaeuk instead of augustus, but according to the user guide, the anaconda metaeuk version does not work for the current BUSCO pipeline. So I installed it manually instead, but it does not seem to be installed as a part of busco (I can see that by typing "busco -h". Normally, there would be optional arguments for metaeuk, but there are none, so busco does not recognize it or something.). Consequently, I decided to just use augustus instead.
There are a few tips regarding augustus in the user guide of BUSCO. For example, it says that I should use the 3.2.3 version and type in "-- augustus" in the command line. In Addtion, there is a section that says that I should set a few variables as the following:

export PATH="/path/to/AUGUSTUS/augustus-3.2.3/bin:$PATH"

export PATH="/path/to/AUGUSTUS/augustus-3.2.3/scripts:$PATH"

export AUGUSTUS_CONFIG_PATH="/path/to/AUGUSTUS/augustus-3.2.3/config/"

I havent done either of them. I use the version 3.3.3., the analysis runs augustus prediction regardless of whether I am typing "-- augutstus" or not and I also did not type in the export commands, because they are part of the section for the Manual installation for BUSCO and I installed it as a conda package, not manually. But is it for some reason I do not know critical to do those steps anyway?

2. Moreover, there is a sentence in the README.md stating "Do not forget to edit the ``config/config.ini`` file to match your environment. The script `scripts/busco_configurator.py` can help with this." I have not run the script because, as I said, I do not want to break something when it is all seemingly working fine right now. I do know what an environment is, but I do not know what is meant by "paths matching my environment". I can find and edit the config file and all the paths that are declared in the file are findable on my computer. So everything should be fine I guess?

I am verry sorry for the long post, but I hope you guys can help me!

Best regards,
Thies

Answer: My question has been answered elsewhere. As assumed, it was totally fine to ignore these steps, thank you for your input!
Unfortunately I do not know how to close a thread, so I will just leave it as it is.