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Top Forums Shell Programming and Scripting Speed up extraction od tar.bz2 files using bash Post 302999126 by cmccabe on Tuesday 13th of June 2017 03:00:52 PM
Old 06-13-2017
The tar.bz2 folders are local. I tried parallel using:

Code:
pbzip2 -dvc folder.tar.bz2 | tar x
pbzip2 -v -d -k -m10500 folder.tar.bz2 | tar x

Those did execute but were really no faster. The second command uses the max allowed 20MB to decompress.

This code is extremely fast but seems to extract partial files within each tar.bz2.

Contents of folder.tar.bz2

Code:
file1.bam -20GB
file2.bam -25GB
file3.bam -19GB
file1.vcf - 10MB
file2.vcf - 8MB
file3.vcf -10MB
file1.bam.bai - 1MB
file2.bam.bai - 1MB
file3.bam.bai - 1 MB

Code:
#!/bin/bash

maxproc=2 # Max number of threads.  Suggest 2, or 3 at most
i=0

# Count files
set -- /home/cmccabe/Desktop/NGS/API/*.tar.bz2
FILES="$#"

# Blank $1 $2 ...
set --

let i=1
for FILE in /home/cmccabe/Desktop/NGS/API/*.tar.bz2
do
        printf "(%2d/%2d)\tProcessing %s\n" "$i" "$FILES" "$FILE"
        let i=i+1

        tar -xvjf "$FILE" -C /home/cmccabe/Desktop/NGS/API >/dev/null &

        # Turn $1=pida $2=pidb $3=pidc $4=pidd, into
        #      $1=pida $2=pidb $3=pidc $4=pidd $5=pide
        set -- "$@" $!

        # Shift removes $1 and moves the rest down, so you get
        # $1=pidb $2=pidc $3=pidd $3=pide
        # $# is the number of arguments.
        if [ "$#" -ge $maxproc ]  ; then wait "$1" ; shift; fi
done

After the code executes:

Code:
file1.bam -15MB
file3.vcf -1MB
file1.bam.bai - 1MB

There may not always be 9 files in each folder, but the file types will always be .bam and .vcf and .bam.bai. Thank you Smilie.
 

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CPAN::Perl::Releases(3pm)				User Contributed Perl Documentation				 CPAN::Perl::Releases(3pm)

NAME
CPAN::Perl::Releases - Mapping Perl releases on CPAN to the location of the tarballs VERSION
version 0.60 SYNOPSIS
use CPAN::Perl::Releases qw[perl_tarballs]; my $perl = '5.14.0'; my $hashref = perl_tarballs( $perl ); print "Location: ", $_, " " for values %{ $hashref }; DESCRIPTION
CPAN::Perl::Releases is a module that contains the mappings of all "perl" releases that have been uploaded to CPAN to the "authors/id/" path that the tarballs reside in. This is static data, but newer versions of this module will be made available as new releases of "perl" are uploaded to CPAN. FUNCTIONS
"perl_tarballs" Takes one parameter, a "perl" version to search for. Returns an hashref on success or "undef" otherwise. The returned hashref will have a key/value for each type of tarball. A key of "tar.gz" indicates the location of a gzipped tar file and "tar.bz2" of a bzip2'd tar file. The values will be the relative path under "authors/id/" on CPAN where the indicated tarball will be located. perl_tarballs( '5.14.0' ); Returns a hashref like: { "tar.bz2" => "J/JE/JESSE/perl-5.14.0.tar.bz2", "tar.gz" => "J/JE/JESSE/perl-5.14.0.tar.gz" } Not all "perl" releases had "tar.bz2", but only a "tar.gz". SEE ALSO
<http://www.cpan.org/src/5.0/> <http://search.cpan.org/faq.html#Is_there_a_API?> AUTHOR
Chris Williams <chris@bingosnet.co.uk> COPYRIGHT AND LICENSE
This software is copyright (c) 2012 by Chris Williams. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. perl v5.14.2 2012-06-20 CPAN::Perl::Releases(3pm)
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