Vm ww viloca automation

[mcarrara-bioinfo]

First version of the automation, re-configured to run on the VM and making full use of the Euler mount for communication with the HPC cluster.
This version already includes the logic necessary to run Viloca automatically on the last available batch.

Important points:

• The system is configured as a docker container, but can be also run directly as a cronjob on the VM. This is done to address concerns regarding the possible side-effects of running the automation in a container
• The system needs to be deployed away from the regular submissions to avoid disruptions
• The system currently DOES NOT backup on the BSSE shared folder because o the suggestion to set up access from Euler instead of from the VM. This needs further discussion
• The system currently always runs Viloca ONLY on the most recent batch available, skipping anything in-between. This needs to be re-worked once Viloca has faster runs

[mcarrara-bioinfo]

Added logic to create a FIFO list of processed batches that the uploader can use.
FIFO used to ensure that new batches are uploaded before anything retrospective