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flass / pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
GNU General Public License v3.0
46 stars 7 forks source link

Dockerfile #11

Closed pveber closed 4 years ago

pveber commented 5 years ago

Use the install script for that.

flass commented 5 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.

samlipworth commented 5 years ago

Is the docker instance ready yet/any idea when it will be?

flass commented 5 years ago

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

bneron commented 5 years ago

the container will be very helpful to run pantagruel on our cluster. thank's Bertrand

pveber commented 5 years ago

stay tuned, it's on its way :o)!

matthieu-haudiquet commented 5 years ago

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

flass commented 4 years ago

: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!