Need general method for uploading many files #5
Description
The Galaxy documentation recommends using FTP for uploading >10 files at once. Unfortunately, there are some complications using FTP with Docker.
(Passive) FTP requires that the FTP server can open arbitrary ports, which isn't feasible with port-mapping. The --net=host option, where "the container shares the host’s networking namespace", can be used instead of port-mapping. This comes with its own complications. First, this comes with security considerations as now all ports opened in Docker are exposed. This may not be an issue within the scope of CloudForest.
Second, because on MacOS Docker actually runs in a VM, the host that shares its networking with the container is actually the VM. This makes it less simple to then interact with the container, e.g. to upload files via FTP.
So, while FTP is viable enough for CloudForest on a Linux server, its may not be great cross-platform.
Another option is SFTP, but the docker-galaxy implementation is not yet secure: bgruening/docker-galaxy#377. For local instances the run.sh script can enable this with the -s flag, and directions for uploading files this way are included in the CloudForest documentation.
One option would be to secure SFTP for shared instances.