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stajichlab / AAFTF

Automatic Assembly For The Fungi
MIT License
19 stars 4 forks source link

After to setup of the requirements, how to install? Is it necessary a sudo user? #11

Closed nickolasmenezes closed 4 years ago

nickolasmenezes commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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