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#!/bin/bash
# These are example SCRIPTs to run PFAM with MPI ON PBS. Minor changes would be needed for LSF etc
# executable for mpirun, e.g. from OpenMPI
MPIRUN_EXEC=`which mpirun`
# these arguments are valid for OpenMPI, change them for Intel's
MPIRUN_ARGS="-gmca mpi_warn_on_fork 0 -cpus-per-proc 1 -np $2 -machinefile workers.$PBS_JOBID.mpi"
#executable of hhmscan
HMMSCAN_EXEC=`which hmmscan`
#your PFAM database
PFAMDB=/home/pap056/30day/databases/pfam/Pfam-AB.hmm.bin
# no need to change the following
export OMP_NUM_THREADS=1
# the PBS_O_WORKDIR is where you launched the script from. Feel free to change this if you need
# to launch it from a difference directory
cd $PBS_O_WORKDIR
cat ${PBS_NODEFILE} > workers.$PBS_JOBID.mpi
$MPIRUN_EXEC $MPIRUN_ARGS ffindex_apply_mpi \
-d "$1"_out2.db \
-i "$1"_out2.db.idx \
$1 \
$1.idx \
-- $HMMSCAN_EXEC -o /dev/null --cpu 1 --noali --cut_nc --acc --notextw --domtblout /dev/stdout $PFAMDB -
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