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README.md

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SplitBlastSlurm

Scripts to multiplex BLAST jobs on a server managed by slurm

Setup

To begin, move this repository with all of its contents into a desired folder. This folder should be in your PATH. Then, run ./install.sh from within this directory. This script sets MASTER_BLASTER_PATH in your ~/.bashrc. Then, you should be able to invoke master_blaster from anywhere on your system.

Usage: master_blaster [options]

Options:

  -h, --help            show this help message and exit
  -q QUERY, --query=QUERY
                        Fasta query file. Can be a comma specified list of
                        fastas also. [None, Required]
  --time 
                        Time to be allotted for each blast job to run. Format
                        is that specified by slurm. [5:00]
  --mem
  	 					Memory to be allotted for each blast job to run.
						[4G]
  --ns=NS, --nucSubject=NS
                        Fasta file of nucleotide sequences to  compare the
                        query sequences to. Will format if necessary. [None]
  --ps=PS, --protSubject=PS
                        Fasta file of protein sequences to compare the query
                        sequences to. Will format if necessary. [None]
  --withColor           Use this flag if you want the colored version of the
                        parsed output to be produced.
  -n NUMPROCS, --numProcs=NUMPROCS
                        Number of separate blasts to start [4]
  -t TEMP, --temp=TEMP  Name for the temporary working directory. Will be
                        created  at the beginning of the script and deleted at
                        the at the end.[/.temp]
  -b BLASTTYPE, --blastType=BLASTTYPE
                        Type of blast to run. Options blastn, blastx, blastp,
                        tblastx, tblastn. [blastn or blastx or blastn, blastx]
  --dontIndex           Use this flag if you don't want the sciprt to try and
                        index the database. This is necessary for complex
                        databases like nt and nr
  --keepOut             Use this flag if you don't want to delete the non-
                        parsed blast files automatically if format not XML]
  --blastFull           Blast full query for each task [automatically used if
                        out format not XML]
  --task=TASK           Type of blastn to run. Options are blastn, dc-
                        megablast, megablast. [megablast, dc-megablast,
                        blastn]
  --evalue=EVALUE       Maximum evalue for hit to be recorded [10]
  -o OUTFMT, --outFmt=OUTFMT
                        Integer specifying the number of blast hits to report
                        per query/subject pair. [5]
  --numHits=NUMHITS     Integer specifying the number of blast hits to report
                        per query. [5]
  --numHsps=NUMHSPS     Integer specifying the number of alignments to report
                        per query/subject pair. [1]
  --goodHit=GOODHIT     Floating point number specifying  the evalue necessary
                        for  a hit to be significant. [0.05]
  --orfSize=ORFSIZE     Integer specifying the minimum size for an open
                        reading frame to be considered significant [100]