Blast++/Batch

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You can submit a blast+ job in batch mode with the following command:

bsub [LSF options] "[blast executable] [blast options]"

Here you need to replace [blast executable] with one of the following executables:

[leonhard@euler05 bin]$ ls
blastdb_aliastool  blastn             deltablast        makembindex           rpstblastn  tblastn
blastdbcheck       blastp             dustmasker        makeprofiledb         seedtop     tblastx
blastdbcmd         blastx             gene_info_reader  project_tree_builder  segmasker   update_blastdb.pl
blastdbcp          convert2blastmask  legacy_blast.pl   psiblast              seqdb_demo  windowmasker
blast_formatter    datatool           makeblastdb       rpsblast              seqdb_perf  windowmasker_2.2.22_adapter.py

Further more, you need to replace [blast options] with blast command line options and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.