Issues for start running the MetaPro

[yeolex]

We have some problems to run the pipeline:

1. In the intructions you say

docker run python3 /pipeline/MetaPro.py -c -1 -2 -o

Is docker run python3 /pipeline/MetaPro.py a command to run MetaPro.py inside a Docker container? If so, should we pull an image and then run the command with -it -v to create a local path within the Docker container? Is the image parkinsonlab/metapro:v3.0.1?

2. In the config.ini file, should the paths to the databases be specified as local paths or container paths? For example:

docker run -it -v /local/path:/container/path parkinsonlab/metapro:v3.0.1 python3 /pipeline/MetaPro.py -c /container/path/config.ini -1 /container/path/forward_read.fastq -2 /container/path/reverse_read.fastq -o /container/path/output_directory

Please don't close this issue yet, as we have more questions to address.

Thanks, and I appreciate your time

[billytaj]

0) each ticket corresponds to each issue. If the issue is related, then feel free to reopen. Otherwise, please issue a new ticket if the context changes. We're trying to keep track of user experiences. It goes to inform us of next directions. Thanks

Also: this question you're asking aren't issues with MetaPro, but with how to use Docker in general. Please see their documentation for further insight. https://docs.docker.com/get-started/introduction/

1) The pipeline is python code, housed inside the docker container., and run inside the docker image. Docker is a software container, similar to virtualboxes .

2) your config file problems are related to your bind-mounting <a fundamental feature in docker that lets the container access paths within your setup/host machine/PC> This isn't something that we can code for everyone, and is 100% a Docker user issue. Not a MetaPro issue.

[yeolex]

Thanks for your answer.

Is the image parkinsonlab/metapro:v3.0.1?

We are working on the entire introduction to Docker and will comment to you as soon as possible.