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Build and run a Docker image executes a nipype workflow that should run an other Docker image that contains the C++ NLMdenoising program of the MIALSRTK library.
Road Map:
Creation of first sinapp workflow with BIDS App parser (python / not containerized yet)
Creation of Dockerfile
Build, test, and make it work
The text was updated successfully, but these errors were encountered:
Access the docker engine of the OS host from within the first container
Solution: Adopting the Docker-out-of-Docker framework maps /var/run/docker.sock into the first container, enabling the first container to access Docker running on the OS host.
It seems we also have to map /usr/bin/docker.
User/group permissions to access the docker.sock mapped within the first container
Solution: Use of docker run -u $(id -u):$(id -g) --group-add 0 to add the current user/group to docker group that seems to be 0.
Access the BIDS dataset from the second container
Solution: Give a name to the first container at execution with docker run --name sinapp_nlmdenoise -v <local/path/to/bids>:/fetaldata that also mounts your local bids directory as the /fetaldata volume of this container and then at the execution of the second container use docker run --volumes-from sinapp_nlmdenoise to be able to access to the volume /fetaldata mount in the first (SINAPP) container.
…Geneva 2019
* Correction of the command to launch the notebook
* Instructions how to use the work developed during the brainhack as an example for the implmentation of the rest of the SINAPPs (Close#5 )
* Update list of contributors
*
Brainhack Global Geneva 2019 Challenge
Build and run a Docker image executes a nipype workflow that should run an other Docker image that contains the C++ NLMdenoising program of the MIALSRTK library.
Road Map:
The text was updated successfully, but these errors were encountered: