Having spent a day in Hyak, I think I know have a workflow that makes sense.

In short, use a date variable to name working directory and sbatch scripts, using rsync from owl to sync mox directory to accessible urls.

1) log into mox.

2) Navigate to user directory

[sr320@mox2 ~]$ cd /gscratch/srlab/sr320/
[sr320@mox2 sr320]$ ls
analyses  blastdb  data  jobs
[sr320@mox2 sr320]$

3) set today variable

today=`date +%m%d_%H%M`

4) Basing sbatch script on prior one.

cp jobs/0804_1818.sh jobs/$today.sh

5) nano to edit

6 set working directory

mkdir analyses/$today

7 ) sbatch -p srlab -A srlab 0804_1818.sh

8) wait, cross fingers, repeat.

9) log into Owl via ssh.

10 sync my mox directory to owl

rsync -avz sr320@mox.hyak.uw.edu:/gscratch/srlab/sr320/ /var/services/web/halfshell/bu-mox/