IBM Platform LSF Cluster at Janelia Research Campus
Janelia Research Campus Configuration
To use, run the pipeline with
-profile janelia. This will download and launch the
janelia.config which has been pre-configured with a setup suitable for the Janelia Research Campus LSF cluster.
Running workflows on the Janelia Research Campus cluster
The latest version of Nextflow is not installed by default on the cluster. You will need to install it into your cluster account by following the installation instructions:
Remember to move the
nextflow executable to
~/bin or otherwise ensure that it’s in your
Nextflow manages each process as a separate job that is submitted to the cluster by using the
bsub command. Janelia’s cluster has Singularity installed on all login and compute nodes, and the profile specifies that Singularity will be used to execute processes.
Nextflow should never be run directly on a login node. You can run it via an interactive cluster session (
bsub -Is /bin/bash), or make a wrapper shell script like the example below, and submit with
bsub < $PWD/my_script.sh