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dellacortelab / prospr

ProSPr: Protein Structure Prediction
MIT License
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I'm unable to run prospr on a sequence #12

Open dante-di opened 4 years ago

dante-di commented 4 years ago

Hello everyone, I installed the ProSPr Docker container.

When I try to run ProSPr on a sequence using the command: docker run -t -v /home/dante/data/:/data prospr/prospr -t --a3mfile /home/dante/data/example1.a3m

I get this error: prospr.py: error: argument command: invalid choice: '/home/dante/data/example1.a3m' (choose from 'run', 'build')

I think I followed the welcome screen directions: To use prospr on your own sequences: docker run -t -v /path/to/local/data:/data prospr/prospr -t --a3mfile /data/my_file.a3m and place a PSIBLAST database under /data/psiblast and a uniclust database under /data/hhblits. ProSPr will download the database if it is missing (250GB and 25GB respectively). Note: I was also unable to download the database.

What am I doing wrong?

Thank you very much, Dante

Lorenzo360 commented 4 years ago

For me a3m files did not work either. However, you can try to put your sequence in a fasta file and do the following. 

mkdir /home/dante/data/example1
cp example1.fasta /home/dante/data/example1/

docker run -it -v /home/Dante/data:/data prospr/prospr build example1
PedroAbilleira commented 3 years ago

I have a somewhat more basic question. I do not know what the folders "/home/dante/data/:/data prospr/prospr" mean. Where are them?