The MouseAtlas software is available on the lonsdale cluster.

Running MouseAtlas

The workflow involves a number of steps, including both interactive GUI steps and batch steps.

Running Interactively

First, log in to lonsdale.

To run interactively, you must submit an interactive job to the queue.

For example, if you're connect from a Linux desktop, use the following to get a SLURM allocation on the interactive 'application' queue for 2 hours, where TCD_XX_YYYYY is your TCHPC project id:

salloc -N 1 -p application -t 2:00:00 -U TCD_XX_YYYYY

Now ssh to the allocated node:

ssh -Y $SLURM_NODELIST

Load the module, and run OptRecon:

[paddy@lonsdale-n144 ~]$ 
[paddy@lonsdale-n144 ~]$ module load apps MouseAtlas
[paddy@lonsdale-n144 ~]$ OptRecon -v -p1 -a5 -e30 -f1 -l676 -ialn -oRecon.wlz

Running in Batch Mode

For the steps like OptRecon which are batch commands and do not require user interaction while running, these can be submitted to the batch queuing system.

You need to create a batch submission script, such as the following (e.g. call it job.sh:

#!/bin/sh
#SBATCH -n 1
#SBATCH -t 00:45:00
#SBATCH -p compute
#SBATCH -U TCD_XX_YYYYY
#SBATCH -J optrecon_job

. /etc/profile.d/modules.sh
module load apps MouseAtlas

echo -n "Running on: "
srun hostname

echo -n "Start time: "
date

# redirect all output to a file called 'out'
OptRecon -v -p1 -a5 -e30 -f1 -l676 -ialn -oRecon.wlz > out 2>&1

echo -n "End time: "
date

And then submit it to the queue as follows:

[paddy@lonsdale01 ~]$ 
[paddy@lonsdale01 ~]$ sbatch job.sh

See these pages for more details on the SLURM batch queuing system.