Currently there are 3 variants of BLAST implementation on hpc2015, namely BLAST+ (serial), mpiBLAST (parallelized using MPI), gpuBLAST (parallelized using single GPU, only supports blastp). This page describes how to use them.

Initial setup

Users are strongly recommended to use the specified paths or have to write their own .ncbirc files

  1. Create the .ncbirc file at your home folder:  bash /share1/blast_common/create_ncbirc_generic.sh
  2. Copy the template folder to scratch folder: cp -r /share1/blast_common/blast_template_folder /data/`whoami`/blast

Structure of the template

/data/username/blast/ : where the job submission templates are
/data/username/blast/database : directory for database files (A 2GB env_nr have been pre-downloaded for the user)
/data/username/blast/queries : directory for database files (A 2GB env_nr have been pre-downloaded for the user)
/data/username/blast/tmp : directory for temporary files of mpiBLAST, should be empty

To use the template

Edit from one of the supplied job submission template. All templates includes an example from formatdb to blast run (or even multiple run), then cleanup of the sorted/pre-formatted databases. If users want to spread BLAST queries into multiple jobs, they are recommended to splot the formatdb and cleanup as two separate jobs so that to save the overhead of preparing such sorted databases.

Running BLAST+: blastplus.cmd
Running mpiBLAST: mpiblast_singleNode.cmd or mpiblast_multiNode.cmd
Running gpuBLAST: gpublast.cmd