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Full Discussion: How to create a variable without multiple concats in a perl scripts that makes a bsub?
Top Forums Shell Programming and Scripting How to create a variable without multiple concats in a perl scripts that makes a bsub? Post 302976744 by jdilts on Tuesday 5th of July 2016 11:15:26 AM
Old 07-05-2016
Facebook How to create a variable without multiple concats in a perl scripts that makes a bsub?
The red text at the bottom represents the three lines I want to address.
I'm dynamically creating a bsub with a perl script and would like to create the
Code:
fasta_16S

variable in a single line....not three. I'm having difficulty in getting the syntax correct. Obviously, there is some confusion because I'm creating a script in a script.

Code:
#!/usr/bin/perl -w


use strict;
use File::Slurp;
use Data::Dumper;




my ($dir,$plugin,$MIN_READ_LENGTH_16S) = @ARGV;
my $microbiome_sample_id_list = $dir . "/sample_ids_of_microbiome_samples.csv";
my $DB="/mnt/Lab/Data/IonTorrent/plugins/" . $plugin . "/db/MB_DB.udb";
my @file = read_file($microbiome_sample_id_list);
my $sample_num = scalar @file;
my $path = "/mnt/Lab/Data/IonTorrent/$server/$run";





open BSUB,">$dir/MB.bsub" || die $!;

       print BSUB "\#!/bin/bash\n

                   \#BSUB -J MBSAMPLE\[1-$sample_num\]
                   \#BSUB -o $path/MBSAMPLE.out
                   \#BSUB -e $path/MBSAMPLE.err\n


                   id=(`sed -n \"\$LSB_JOBINDEX\"p $path/sample_ids_of_microbiome_samples.csv`)

                   fasta_16S=$path/\${id}/\${id}_bacterial_minreadlen
                   fasta_16S+=$MIN_READ_LENGTH_16S
                   fasta_16S+=.fasta

              ";

close(BSUB);

 

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LEARN ABOUT DEBIAN

file::slurp::withinpolicy

File::Slurp::WithinPolicy(3pm)				User Contributed Perl Documentation			    File::Slurp::WithinPolicy(3pm)

NAME

       File::Slurp::WithinPolicy - Applies filesystem policies to File::Slurp

SYNOPSIS

	 use File::Slurp::WithinPolicy qw(:all);

	 my $text = read_file( 'filename' );
	 my @lines = read_file( 'filename' );
	 write_file( 'filename', $text );
	 append_file( 'filename', $more_text );
	 overwrite_file( 'filename', $text );
	 my @files = read_dir( '/path/to/dir' );

DESCRIPTION

       This provides the File::Slurp interface within a policy defined by File::Policy.  By default, File::Policy is a no-op and this behaves
       identically to File::Slurp.  System administrators may want to override the default File::Policy implementation to enforce a local filesys-
       tem policy (see File::Policy).

FUNCTIONS

       read_dir

       See "read_dir" in File::Slurp

       read_file

       See "read_file" in File::Slurp

       write_file

       See "write_file" in File::Slurp

       append_file

       See "append_file" in File::Slurp

       overwrite_file

       See "overwrite_file" in File::Slurp

EXPORTS

       By default, nothing is exported.  The ":all" tag can be used to export everything.  Individual methods can also be exported.

SEE ALSO

       File::Slurp, File::Policy

VERSION

       $Revision: 1.4 $ on $Date: 2005/06/15 10:40:21 $ by $Author: simonf $

AUTHOR

       John Alden <cpan _at_ bbc _dot_ co _dot_ uk>

COPYRIGHT

       (c) BBC 2005. This program is free software; you can redistribute it and/or modify it under the GNU GPL.

       See the file COPYING in this distribution, or http://www.gnu.org/licenses/gpl.txt

perl v5.8.8							    2005-06-15					    File::Slurp::WithinPolicy(3pm)
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