How to create a variable without multiple concats in a perl scripts that makes a bsub? Post: 302976744

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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

07-05-2016

Registered User

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

pperl

PPERL(1p)						User Contributed Perl Documentation						 PPERL(1p)

NAME

       PPerl - Make perl scripts persistent in memory

SYNOPSIS

	 $ pperl foo.pl

DESCRIPTION

       This program turns ordinary perl scripts into long running daemons, making subsequent executions extremely fast. It forks several processes
       for each script, allowing many processes to call the script at once.

       It works a lot like SpeedyCGI, but is written a little differently. I didn't use the SpeedyCGI codebase, because I couldn't get it to
       compile, and needed something ASAP.

       The easiest way to use this is to change your shebang line from:

	 #!/usr/bin/perl -w

       To use pperl instead:

	 #!/usr/bin/pperl -w

WARNINGS

       Like other persistent environments, this one has problems with things like BEGIN blocks, global variables, etc. So beware, and try checking
       the mod_perl guide at http://perl.apache.org/guide/ for lots of information that applies to many persistent perl environments.

Parameters
	 $ pperl <perl params> -- <pperl params> scriptname <script params>

       The perl params are sent to the perl binary the first time it is started up.  See perlrun for details.

       The pperl params control how pperl works. Try -h for an overview.

       The script params are passed to the script on every invocation. The script also gets any current environment variables, the current working
       directory, and everything on STDIN.

Killing
       In order to kill a currently running PPerl process, use:

	 pperl -- -k <scriptname>

       You need to make sure the path to the script is the same as when it was invoked.

       Alternatively look for a .pid file for the script in your tmp directory, and kill (with SIGINT) the process with that PID.

ENVIRONMENT

       pperl uses the PPERL_TMP_PATH environment variable to determine the directory where to store the files used for inter-process
       communication.  By default, the subdirectory .pperl of the user's home directory is used.

BUGS

       The process does not reload when the script or modules change.

       $^S is not represented identically with respect to perl, since your script will be run within an eval block

AUTHOR

       Matt Sergeant, matt@sergeant.org. Copyright 2001 MessageLabs Ltd.

SEE ALSO

       perl. perlrun.

perl v5.14.2							    2011-11-15								 PPERL(1p)

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