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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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BAM(1)								   User Commands							    BAM(1)

NAME
bam - fast and flexible build system SYNOPSIS
bam [OPTION]... [VARIABLE=VALUE]... [TARGET]... DESCRIPTION
Builds applications using the bam build system. Execution: -a abort on error -c clean targets -d build targets that is dependent given targets --dry dry run, don't run any jobs -j sets the number of threads to use (default: 0, disabled) -s bam file to use (default: bam.lua) Lua: -l print local variables in backtrace -t print backtrace when an error occurs Output: -r build progress report format (default: s) b = progress bar c = use ansi colors s = build steps -v be verbose Other: -n don't use cache -h, --help prints this help Debug: --debug-nodes prints all the nodes with dependencies --debug-detail prints all the nodes with dependencies and details --debug-jobs prints all the jobs that exist --debug-dot prints all nodes as a graphviz dot file --debug-jobs-dot prints all jobs as a graphviz dot file --debug-trace-vm prints a line for every instruction the vm makes --debug-dump-int prints the internals scripts to stdout --debug-no-int don't load internal scripts bam by Magnus Auvinen (magnus.auvinen@gmail.com) bam May 2011 BAM(1)
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