Using LSF with NCBI BLAST

LSF accepts jobs running NCBI BLAST (Basic Local Alignment Search Tool).

Configuring LSF for BLAST

To configure LSF for BLAST:

LSF HPC features must be enabled.
BLAST, available from the National Center for Biotechnology Information (NCBI) , must be installed.

During installation, lsfinstall adds the Boolean resource blast to the Resource section of lsf.shared.

If only some of your hosts can accept BLAST jobs, configure the Host section of lsf.cluster.cluster_name to identify those hosts.

Edit LSF_ENVDIR/conf/lsf.cluster.cluster_name file and add the blast resource to the hosts that can run BLAST jobs:

Begin Host
HOSTNAME    model   type  server  r1m   mem   swp  RESOURCES
...
hostA       !       !       1     3.5   ()    ()   ()
hostB       !       !       1     3.5   ()    ()   (blast)
hostC       !       !       1     3.5   ()    ()   ()
...
End Host

Submitting BLAST jobs

Use BLAST parallel provided with LSF to submit BLAST jobs.

BLAST parallel is a PERL program that distributes BLAST searches across a cluster by splitting both the query file and the reference database and merging the result files after all BLAST jobs finish.

See the README in the LSF_MISC/examples/blastparallel/ for information about installing, configuring, and using BLAST parallel.

The Selected Product dialog shows the following information: