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Cellprofiler on NIH HPC Systems

CellProfiler is open-source software helping biologists turn images into cell measurements.It is designed to serve biologists as well as bioimage analysts who want a flexible system that is easy to deploy to collaborators who lack computational skills. It is commonly used for small-scale experiments involving a few images but is also routinely run on millions of images using cluster or cloud computing resources at some of the largest pharmaceutical companies and academic screening centers in the world.

On Helix

Sample session:


[helix ~]$ module load cellprofiler
[helix ~]$ cellprofiler command

Batch job on Biowulf

Create a batch input file (e.g. script.sh). For example:

#!/bin/bash
module load cellprofiler

cd /data/$USER/dir
cellprofiler command 1
cellprofiler command 2
......

Then submit the file on biowulf

biowulf> $ sbatch script.sh

For more information regarding sbatch command : https://hpc.nih.gov/docs/userguide.html#submit

Swarm of Jobs on Biowulf

Create a swarmfile (e.g. script.swarm). For example:

# this file is called script.swarm
cd dir1;cellprofiler command 1; cellprofiler command 2
cd dir2;cellprofiler command 1; cellprofiler command 2
cd dir3;cellprofiler command 1; cellprofiler command 2
[...]

Submit this job using the swarm command.

swarm -f script.swarm --module parpipe

For more information regarding swarm: https://hpc.nih.gov/apps/swarm.html#usage

Interactive job on Biowulf

Allocate an interactive session. Sample session:

[biowulf ~]$ sinteractive --mem=5g
salloc.exe: Pending job allocation 15194042
salloc.exe: job 15194042 queued and waiting for resources
salloc.exe: job 15194042 has been allocated resources
salloc.exe: Granted job allocation 15194042
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1719 are ready for job

[cn1719 ~]$ module load cellprofiler

[cn1719 ~]$ cellprofiler command
Documentation
http://cellprofiler.org/tutorials/