tim488
commented
2 years ago Hi Marie,
think of the docker container (where the running program MeTaPONT lives) as a small separated part of your computer.
It is separated from the file structure. That's why we need to map the files that MeTaPONT needs to the inside of the Container. The -v parameter does this (for detailed descriptions about volume mounting have a look here). So MeTaPONT always looks for the database i.e. the *.cf files in the /database/ directory (which is inside the Docker Container). The files should be there because we map them there with -v /home/marie/some/path/to/database/:/database .
Following the instructions, you probably need to use
docker run -v /home/marie/Tools/MeTaPONT/2018_pro:/database -v /home/marie/Tools/MeTaPONT/barcode01:/input /home/marie/Tools/MeTaPONT/TEST1:/output metapont
I hope this makes sense to you.
Note how I changed the relative paths to absolute paths (you probably need to change the username, depending on your machine, you may use echo ~ in the terminal to find the absolute path to your home directory ~). Absolute paths are needed by Docker.
Please feel free to ask further questions! Cheers, Tim :-)
marieleoz
Hello,
I'm not very familiar with Docker, and not at all with Centrifuge yet, but I'd like to try MeTaPONT on some 16S reads from Nanopore. I decided to first test it with the prebuilt library you provide, which I downloaded, unzipped and extracted to a folder with the following path: ~/Tools/MeTaPONT/2018_pro/
I tried several commands deriving from the one you indicate: Docker run -v /path/to/database:/database -v /path/to/input:/input -v /path/to/output/directory:/output ContainerName [Parameters] Finally got something running with this: docker run metapont ~/Tools/MeTaPONT/2018_pro ~/Tools/MeTaPONT/barcode01 ~/Tools/MeTaPONT/TEST1
But it looks like it's not ok since I got: (...) find: '*.cf': No such file or directory Could not locate a Centrifuge index corresponding to basename "/database//" (...)
(See all the stdout / stderr attached) test1_stdout_stderr.txt
I've tried quite a lot of variations of this command, and especially on how to express: -v /path/to/database:/database But I am stuck. Could you help please?
Thanks! Marie