Broadly similar to SciNet, except that there's no need to wrap rsync commands in a loop since there's no hard CPU time limit on the login nodes, though again you may benefit from running
screen as per above..
For transferring data such as your input
.mnc files, you can use
rsync as usual:
scp -r /hpf/largeprojects/MICe/yourname/inputfiles/ firstname.lastname@example.org:/scratch/yourname
Your main disk spaces are $HOME, $SCRATCH, and $PROJECT. $HOME is small and should be used mostly for text files, etc. $SCRATCH should be used for running pipelines. It is not backed up and inactive files are deleted regularly (you will receive email prior to any deletion). $PROJECT can be used for storing completed pipelines and analyses.