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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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latest docker image not working #78

Closed ccshao closed 4 years ago

ccshao commented 4 years ago

Thanks for new version. I am trying the docker image on mac, with the latest docker desktop. First download the image docker pull pinellolab/stream

However, docker failed to run it.

docker run pinellolab/stream

docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "exec: \"stream\": executable file not found in $PATH": unknown. ERRO[0000] error waiting for container: context canceled

I am very new to docker. Are there additial steps needed before running the image? Thanks!

huidongchen commented 4 years ago

Hi,

As mentioned in our release note, from v1.0 we do not support command line interface anymore since a one-size-fits-all solution is not desirable.

To use the latest version, you can:

1) (Easier version): install our bioconda package and follow our latest tutorials as before

2) (Complicated version): to use our docker image, you will have to enter docker container and mount your input data. so basically you will need to run two steps:

$ docker run --entrypoint /bin/bash -v /your/data/file/path/:/data -w /data -p 8888:8888 -it pinellolab/stream:1.0

Once you are in the container, you can start Jupyter notebook by executing: jupyter notebook --ip 0.0.0.0 --port 8888 --no-browser --allow-root

ccshao commented 4 years ago

Thanks for the quick updates :)