After to setup of the requirements, how to install? Is it necessary a sudo user?

[nickolasmenezes]

Hi dear all,

I'm trying to use, but I did not find instructions to setup the AAFTF after the requirements.
I cloned the repository and added to the path, but did not work.
Could you please send me some instructions?

Thank you.
Kind regards
Nickolas

[hyphaltip]

For now, until I finish making a conda package, is you just need to make sure the 'scripts' folder is in your PATH. eg
on my system we have the folder /folder/to/AAFTF/scripts added to PATH.

Did you also install dependencies? At a minimum you need SPAdes, pilon, ncbi-blast, BBMap, and samtools -- alternative trimmomatic.

[nickolasmenezes]

Hi @hyphaltip

Thanks a lot. Conda package will be great. Congratulations.
I had set the path to /folder/to/AAFTF/. Now, it's working.
Maybe you can add this information in the Readme.txt.

Yes, I configured all dependencies already.
Kind regards.

[hyphaltip]

will be adding more - I don't consider this an official release yet so I have not finished the packaging and documentation intended to be used by a broader user base just yet but I can add to the docs. Not enough time in the day to keep up with all these needs, sorry!

[nickolasmenezes]

Don't worry. I can understand.
You do a great job.
Marcus Teixeira recommends this pipeline to me.
Good Luck