Bowtie Code

137 lines (116 with data), 6.6 kB

#!/usr/bin/perl -w

##
# Author: Ben Langmead
#   Date: February 11, 2010
#
# Use 'elastic-mapreduce' ruby script to invoke an EMR job described
# in a dynamically-generated JSON file.  Constructs the elastic-
# mapreduce invocation from paramteres/defaults/environment variables.
#

use strict;
use warnings;

use FindBin qw($Bin);
use lib $Bin;
use CrossbowIface;

my $APP = "Crossbow";
my $app = lc $APP;
my $SCRIPT = "cb_emr";
my $VERSION = `cat $Bin/VERSION`; $VERSION =~ s/\s//g;

my $usage = qq{
$SCRIPT: Run $APP v$VERSION as an Elastic MapReduce job

Usage: perl $SCRIPT --input <url> --output <url> \
                    [--reference <url> | --just-preprocess ] [options]

Options (defaults in []):

 EMR params:

  --credentials <path>   Path to credentials.json file [elastic-mapreduce
                         script's default]
  --emr-script <path>    Path to 'elastic-mapreduce' script [First under
                         \$${APP}_EMR, then in \$PATH]
  --hadoop-version <ver> Hadoop version to use on EMR; for now, the options are
                         0.18 and 0.20 [0.20]
  --dry-run              Produce job's .json and .sh files and print
                        'elastic-mapreduce' command but don't run it
  --name <name>          Name for EMR job ["$APP"]
  --stay-alive           Keep cluster running even if it completes or a step
                         fails [off]
  --instance-type <type> EC2 instance type [c1.xlarge (highly recommended)]
  --nodes <int>          Number of nodes (instances) to allocate [1]
  --emr-args "<args>"    Extra arguments for 'elastic-mapreduce' script [none]
  --logs <url>           By default, logs are deposited in 'log' directory
                         alongside the --output URL.  Override by specifying
                         --logs and an S3 URL. Can't be a subdirectory of
                         --output.
  --no-logs              Disables copying of logs entirely [off]
  --no-emr-debug         Disable SimpleDB-based debugging.  SimpleDB-based
                         debugging enables the "Debug" button in the AWS
                         Console.  User must have SimpleDB account when this is
                         *not* specified. [off]

 Job params (don't affect results):

  --input <url>          S3 URL for input.  Usually a directory with
                         preprocessed reads.  If --preprocess or
                         --just-preprocess are specified, URL is a manifest
                         file.
  --output <url>         Final output (S3)
  --intermediate <url>   Intermediate output (can be HDFS, S3).  Use an S3 URL
                         if you'd like keep to keep intermediate results after
                         cluster is deallocated. [hdfs:///$app/intermediate]
  --partition-len <int>  Partition length in bases [1 million]

 $APP params (affect results):

  --reference <url>      Reference jar (can be HDFS, S3, local, HTTP, FTP)
  --quality <type>       Encoding for sequence quality values; one of: phred33,
                         phred64, solexa64 [phred33]
  --just-align           Don't do SNP calling; --output will contain alignments
  --resume-align         --input URL is a directory of output from the Crossbow
                         alignment step (obtained e.g. using --intermediate);
                         pipeline resumes at the SNP calling step
  --resume-snps          --input URL is a directory of output from the Crossbow
                         SNP calling step (obtained e.g. using --intermediate);
                         pipeline resumes at post-SNP-calling sort step
  --bowtie-args "<args>" Arguments for Bowtie [-M 1] (Note: --partition --mm -t
                         --hadoopout --startverbose are always set by Crossbow)
  --ss-args "<args>"     Arguments for SOAPsnp [-2 -u -n -q] (Note: -i -d -o -s
                         -z -L -T are always set by Crossbow)
  --ss-hap-args "<args>" Additional SOAPsnp arguments when reference is haploid
                         [-r 0.0001] (Note: -m is always set by Crossbow)
  --ss-dip-args "<args>" Additional SOAPsnp arguments when reference is diploid
                         [-r 0.00005 -e 0.0001]
  --haploids "<chrs>"    Comma-separated names of references that are haploid.
                         Others are considered diploid. [All diploid].
  --all-haploids         Consider all chromosomes to be haploid when calling
                         SNPs. [All diploid]
  --discard-reads <frac> Randomly discard specified fraction of input reads.
                         [off]
  --truncate <int>       Truncate reads longer than <int> bases to <int> bases
                         by trimming from the 3' end [off]
  --truncate-discard <int> Same as --truncate except that reads shorter than
                         <int> bases are discarded. [off]

  Preprocessing params (not necessary if --input points to preprocessed reads):

  --preprocess           --input URL is a manifest file describing a set of
                         unpreprocessed, FASTQ read files; preprocess them
                         before running $APP [off]
  --just-preprocess      Like --preprocess but $APP isn't run; --output
                         contains preprocessed reads [off]
  --pre-output <url>     If --preprocess is on, put preprocessed output here
                         instead of in the intermediate directory [off].  Has
                         no effect if --just-preprocess is specifeid (use
                         --output). Useful if future jobs will make use of the
                         same input.
  --pre-compress <type>  Compression type; one of: gzip, none [gzip]
  --pre-stop <int>       Stop preprocessing after <int> reads/mates [no limit]
  --pre-filemax <int>    Split preprocessed output such that there are no more
                         than <int> reads/mates per preprocessed read file;
                         0 = no limit. [500,000]

  Other params:

  --test                 Try to locate all necessary software; print a helpful
                         message showing what was found and quit [off]
  --tempdir <path>       Put temporary scripts and files in <path> [/tmp]

};

# Try to avoid forcing the user to use the equals sign in cases where
# they're specifying a set of arguments, as in --bowtie-args "-n 3 -l 35"
for(my $i = 0; $i < scalar(@ARGV)-1; $i++) {
	if($ARGV[$i] =~ /^-.*-args$/) {
		$ARGV[$i] = "$ARGV[$i]=\"".$ARGV[$i+1]."\"";
		splice @ARGV, $i+1, 1;
	}
}

CrossbowIface::crossbow(\@ARGV, $SCRIPT, $usage, undef, undef, undef, undef);