NAME

       makeflow_blast - Generate a Makeflow to parallelize and distribute blastall jobs

SYNOPSIS

       makeflow_blast query_granularity character_granularity [blast_options]

DESCRIPTION

       makeflow_blast  is  a  script  to  generate makeflow() workflows to execute blastall jobs.
       Essentially, the script uses query_granularity (the maximum number of sequences per  fasta
       file  split)  and  character_granularity  (the maximum number of characters per fasta file
       split) to determine how to break up the input fasta file.  It then creates a makeflow that
       will  execute  a  blastall  with  the  desired parameters on each part and concatenate the
       results into the desired output file.  For simplicity,  all  of  the  arguments  following
       query_granularity and character_granularity are passed through as the options to blastall

       makeflow_blast  executes a small test BLAST job with the user provided parameters in order
       to be sure that the given parameters are sane.  It then calculates the number of parts the
       provided  fasta  input  file  will require, prints a makeflow rule to generate those parts
       using split_fasta(), and enumerates makeflow rules to  execute  blastall  with  the  given
       parameters on each part. Subsequent rules to condense and clean the intermediate input and
       output are then produced.

       makeflow_blast expects a blastall in the path, and  should  be  used  from  the  directory
       containing  the  input  files and databases.  For distribution convenience, it is required
       that the files constituting a given BLAST database must be stored in  a  folder  with  the
       same name as that database.

OPTIONS

        -i <input>
              Specifiy the input fasta file for querying the BLAST database

        -o <output>
              Specify the output file for final results

        -d <databse>
              Specify the BLAST database to be queried

EXIT STATUS

       On success, returns zero.  On failure, returns non-zero.

ENVIRONMENT VARIABLES

EXAMPLES

       To  generate  a  makeflow  to  run blastall -p blastn on smallpks.fa and testdb, splitting
       smallpks.fa every 500 sequences or 10000 characters and  placing  the  blast  output  into
       test.txt do:

               python makeflow_blast 500 10000 -i smallpks.fa -o test -d testdb/testdb -p blastn > Makeflow

       You  can  then execute this workflow in a variety of distributed and parallel environments
       using the makeflow command.

COPYRIGHT

       The Cooperative Computing Tools are Copyright (C) 2005-2019 The University of Notre  Dame.
       This  software  is distributed under the GNU General Public License.  See the file COPYING
       for details.

SEE ALSO

       •   Cooperative Computing Tools Documentation

       •   Makeflow User Manual

       •   makeflow(1)       makeflow_monitor(1)       makeflow_analyze(1)        makeflow_viz(1)
           makeflow_graph_log(1)    starch(1)    makeflow_ec2_setup(1)    makeflow_ec2_cleanup(1)
           makeflow_ec2_estimate(1)