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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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merge(1)																  merge(1)

NAME
merge - three-way file merge SYNOPSIS
merge [-Llabel1 [-Llabel3]] [-p] [-q] file1 file2 file3 DESCRIPTION
merge incorporates all changes that lead from file2 to file3 into file1. The result goes to standard output if -p is present, into file1 otherwise. merge is useful for combining separate changes to an original. Suppose file2 is the original, and both file1 and file3 are modifications of file2. Then merge combines both changes. An overlap occurs if both file1 and file3 have changes in a common segment of lines. On a few older hosts where diff3 does not support the -E option, merge does not detect overlaps, and merely supplies the changed lines from file3. On most hosts, if overlaps occur, merge out- puts a message (unless the -q option is given), and includes both alternatives in the result. The alternatives are delimited as follows: <<<<<<< file1 lines in file1 ======= lines in file3 >>>>>>> file3 If there are overlaps, the user should edit the result and delete one of the alternatives. If the -L label1 and -L label3 options are given, the labels are output in place of the names file1 and file3 in overlap reports. DIAGNOSTICS
Exit status is 0 for no overlaps, 1 for some overlaps, 2 for trouble. IDENTIFICATION
Author: Walter F. Tichy. Revision Number: 1.1.6.2; Release Date: 1993/10/07. Copyright (C) 1982, 1988, 1989 by Walter F. Tichy. Copyright (C) 1990, 1991 by Paul Eggert. SEE ALSO
diff3(1), diff(1), rcsmerge(1), co(1) merge(1)
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