Closed pveber closed 4 years ago
(rephrasing to external readers:)
We should soon release a Docker instance that contains all the dependencies (so no need to install anything), within which you will be able to run Pantagruel scripts (i.e. execute the commands pantagruel --options TASK
).
Further integration of the Pantagruel pipeline into a Docker or Singularity container will later follow, so that the runtime is also handled, making the containers more like proper apps.
Is the docker instance ready yet/any idea when it will be?
Dear Sam, sorry for the wait. the Docker file is almost done. We were fighting with the integration of Interproscan (required for task 4), which we may have to exclude from the first packaged version. We should hopefully come back to you soon with the Dockerfile ready! BW, Florent
the container will be very helpful to run pantagruel on our cluster. thank's Bertrand
stay tuned, it's on its way :o)!
Dear Sam, sorry for the wait. the Docker file is almost done. We were fighting with the integration of Interproscan (required for task 4), which we may have to exclude from the first packaged version. We should hopefully come back to you soon with the Dockerfile ready! BW, Florent
If it's of any help :-)
https://github.com/Micromeda/InterProScan-Docker
https://github.com/biocorecrg/interproscan_docker/blob/master/Singularity
:whale: The Dockerfile is now available!
Use it to generate a Docker image containing all Pantagruel dependencies; then use that image to run pantagruel
commands within the environment provided by the container, as explained here.
NB: this may be used to generate a Singularity container as well, even though it was not tested yet
The Docker image is being validated (currently fixing task 08, but that's only at the pipeline script level, the dependencies and thus the Docker image are fine); once this is done, I'll consider providing an already compiled image (e.g. via dockerhub).
Feel free to comment and post issue regarding the use of the container version!
Use the install script for that.