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[r9]: / myrna / myrna_hadoop Maximize Restore History
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#!/usr/bin/perl -w
##
# Author: Ben Langmead
# Date: February 11, 2010
#
# Initiate a Hadoop streaming Crossbow job. Must be on the Hadoop master node.
#
use strict;
use warnings;
use Getopt::Long qw(:config pass_through);
use FindBin qw($Bin);
use lib $Bin;
use MyrnaIface;
use Cwd 'abs_path';
my $APP = "Myrna";
my $app = lc $APP;
my $SCRIPT = "myrna_hadoop";
my $VERSION = `cat $Bin/VERSION`; $VERSION =~ s/\s//g;
my $usage = qq{
$SCRIPT: Run $APP v$VERSION as a Hadoop job
Usage: perl $SCRIPT --input <url> --output <url> \
[--reference <url> | --just-preprocess ] [options]
Options (defaults in []):
Job params:
--dry-run Produce and print path to a script for running the
Hadoop job, but don't run it.
--input <url> HDFS or S3 URL for input. URL is typically a
directory containing preprocessed reads. If
--preprocess or --just-preprocess are enabled, URL is
a manifest file. If --resume-align is enabled, URL is
a directory containing $APP alignments.
--output <url> Final output (can be HDFS, 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:///crossbow]
--partition-len <int> Partition length in bases [1 million]
--bowtie <path> Path to bowtie binary on slaves [search
\$MYRNA_BOWTIE_HOME, \$MYRNA_HOME/bin, \$PATH locally]
--Rhome <path> R home on slaves [search \$MYRNA_RHOME, \$MYRNA_HOME/R,
\$PATH locally]
$APP params (affect results):
--reference <path> Path to directory with reference information (must be
local, with "index", and "ivals" subdirs)
--bin <int> If set, Myrna uses non-overlapping genomic bins
instead of gene/exon intervals. <int> = bin width
[off]. If used with --sam-passthrough, --reference
need not be specified.
--top <int> Make plots and save alignments for <int> genes with
lowest P values [50]
--test <family> Statistical family to use for differential expression
test; one of: "poisson", "gaussian" [poisson]
--norm <type> Per-gene count normalization scheme to use; one of:
"upper-quartile", "median", "total" ["upper-quartile"]
--ival-model <type> Interval model used to model genes; one of: "union",
"union-constitutive", "union-intersection"
["union-intersection"]
--influence <int> Maximum "influence" per alignment. If alignment
length is < <int>, overlaps are calculated as if
length = <int> [1]
--from5prime Measure read's influence from the 5' end [from 3' end]
--sam-passthrough Re-use SAM's alignments instead of calculating new
ones. If used with --bin, --reference need not be
specified.
--sam-lab-rg When --sam-passthrough is specified, set each read's
label equal to the value of the RG:Z optional field.
--just-align Stop after alignment; alignments put in --output [off]
--just-count Don't do normalization or statistics; --output will
just contain per-gene counts [off]
--resume-align --input URL is an S3 intermediate directory from a
previous run; pipeline resumes before overlapping
[off]
--resume-olaps --input URL is an S3 intermediate directory from a
previous run; resumes before normalization [off]
--resume-normal --input URL is an S3 intermediate directory from a
previous run; resumes before statistics [off]
--resume-stats --input URL is an S3 intermediate directory from a
previous run; resumes before summarization [off]
--resume-summ --input URL is an S3 intermediate directory from a
previous run; resumes before postprocessing [off]
--bowtie-args "<args>" Arguments for Bowtie [-m 1] (Note: --partition --mm -t
--hadoopout --startverbose are always set by $APP)
--bypass-pvals Don't calculate interval stastics; all intervals get a
differential expression P-value of 1. [off]
--quality <type> Encoding for sequence quality values; one of: phred33,
phred64, solexa64 [phred33]
--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.
--truncate-discard <int> Same as --truncate except that reads shorter than
<int> bases are discarded.
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 $APP isn't run; --output
contains preprocessed reads [off]
--pre-output <url> If --preprocess is on, put preprocessed output here
instead of in the intermediate directory [off]. Has
no effect if --just-preprocess is specified (--output
is used instead). Useful if future jobs use same
input.
--pre-compress <type> Compression type; one of: gzip, none [gzip]
--pre-stop <int> Stop preprocessing after <int> reads/mates [no limit]
--pre-filemax <int> Split preprocessed output such that there are no more
than <int> reads/mates per preprocessed read file;
0 = no limit. [500,000]
Other params:
--test Try to locate all necessary software; print a helpful
message showing what was found and quit [off]
--tempdir <path> Put temporary scripts in <path>
[/tmp/$APP/invoke.scripts]
(umask 0077 used to protect credentials)
};
sub dieusage($$$) {
my ($text, $usage, $lev) = @_;
print STDERR "$usage\nError:\n";
print STDERR "$text\n\n";
exit $lev;
}
# Try to avoid forcing the user to use the equals sign in cases where
# they're specifying a set of arguments, as in --bowtie-args "-n 3 -l 35"
for(my $i = 0; $i < scalar(@ARGV)-1; $i++) {
if($ARGV[$i] =~ /^-.*-args$/) {
$ARGV[$i] = "$ARGV[$i]=\"".$ARGV[$i+1]."\"";
splice @ARGV, $i+1, 1;
}
}
my $input = "";
my $output = "";
my $intermediate = "";
my $ref = "";
my $bowtie = "";
my $Rhome = "";
my $samtools = "";
my $verbose = 0;
my $test = 0;
GetOptions (
"input:s" => \$input,
"output:s" => \$output,
"intermediate:s" => \$intermediate,
"reference:s" => \$ref,
"Rhome:s" => \$Rhome,
"bowtie:s" => \$bowtie,
"samtools:s" => \$samtools,
"test" => \$test,
"verbose" => \$verbose
);
##
# Take a path and make it absolute. If it has a protocol, assume it's
# already absolute.
#
sub absPath($$$) {
my ($path, $check, $name) = @_;
return $path if $path =~ /^s3n?:\//i;
return $path if $path =~ /^hdfs:\//i;
return $path if $path =~ /^file:\//i;
$path =~ s/^~/$ENV{HOME}/;
die "Error: $name path doesn't exist: $path" unless (!$check || -f $path || -d $path);
return abs_path($path);
}
if($verbose) {
print STDERR "Relative paths:\n";
print STDERR " input: $input\n";
print STDERR " output: $output\n";
print STDERR " intermediate: $intermediate\n";
print STDERR " reference: $ref\n";
print STDERR " Rhome: $Rhome\n";
print STDERR " bowtie: $bowtie\n";
print STDERR " samtools: $samtools\n";
}
$input = absPath($input, 1, "--input") if $input ne "";
$output = absPath($output, 0, "--output") if $output ne "";
$intermediate = absPath($intermediate, 0, "--intermediate") if $intermediate ne "";
$ref = absPath($ref, 1, "--reference") if $ref ne "";
$Rhome = absPath($Rhome, 1, "--Rhome") if $Rhome ne "";
$bowtie = absPath($bowtie, 1, "--bowtie") if $bowtie ne "";
$samtools = absPath($samtools, 1, "--samtools") if $samtools ne "";
if($verbose) {
print STDERR "Absolute paths:\n";
print STDERR " input: $input\n";
print STDERR " output: $output\n";
print STDERR " intermediate: $intermediate\n";
print STDERR " reference: $ref\n";
print STDERR " Rhome: $Rhome\n";
print STDERR " bowtie: $bowtie\n";
print STDERR " samtools: $samtools\n";
}
if(!$test) {
$input ne "" || dieusage("Must specify --input", $usage, 1);
$output ne "" || dieusage("Must specify --output", $usage, 1);
}
my @args = ();
push @args, "--hadoop-job";
push @args, ("--input", $input) if $input ne "";
push @args, ("--output", $output) if $output ne "";
push @args, ("--intermediate", $intermediate) if $intermediate ne "";
push @args, ("--reference", $ref) if $ref ne "";
push @args, ("--Rhome", $Rhome) if $Rhome ne "";
push @args, ("--bowtie", $bowtie) if $bowtie ne "";
push @args, ("--samtools", $samtools) if $samtools ne "";
push @args, "--verbose" if $verbose;
push @args, "--test" if $test;
$ref ne "" || $test || die "Must specify --reference\n";
push @args, @ARGV;
MyrnaIface::myrna(\@args, $SCRIPT, $usage, undef, undef, undef, undef);