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) 2003-2004 Douglas Thain and Copyright (C) 2005-2015 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)