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)