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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
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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Plack::App::CGIBin(3pm) 				User Contributed Perl Documentation				   Plack::App::CGIBin(3pm)

NAME
Plack::App::CGIBin - cgi-bin replacement for Plack servers SYNOPSIS
use Plack::App::CGIBin; use Plack::Builder; my $app = Plack::App::CGIBin->new(root => "/path/to/cgi-bin")->to_app; builder { mount "/cgi-bin" => $app; }; # Or from the command line plackup -MPlack::App::CGIBin -e 'Plack::App::CGIBin->new(root => "/path/to/cgi-bin")->to_app' DESCRIPTION
Plack::App::CGIBin allows you to load CGI scripts from a directory and convert them into a PSGI application. This would give you the extreme easiness when you have bunch of old CGI scripts that is loaded using cgi-bin of Apache web server. HOW IT WORKS
This application checks if a given file path is a perl script and if so, uses CGI::Compile to compile a CGI script into a sub (like ModPerl::Registry) and then run it as a persistent application using CGI::Emulate::PSGI. If the given file is not a perl script, it executes the script just like a normal CGI script with fork & exec. This is like a normal web server mode and no performance benefit is achieved. The default mechanism to determine if a given file is a Perl script is as follows: o Check if the filename ends with ".pl". If yes, it is a Perl script. o Open the file and see if the shebang (first line of the file) contains the word "perl" (like "#!/usr/bin/perl"). If yes, it is a Perl script. You can customize this behavior by passing "exec_cb" callback, which takes a file path to its first argument. For example, if your perl-based CGI script uses lots of global variables and such and are not ready to run on a persistent environment, you can do: my $app = Plack::App::CGIBin->new( root => "/path/to/cgi-bin", exec_cb => sub { 1 }, )->to_app; to always force the execute option for any files. AUTHOR
Tatsuhiko Miyagawa SEE ALSO
Plack::App::File CGI::Emulate::PSGI CGI::Compile Plack::App::WrapCGI See also Plack::App::WrapCGI if you compile one CGI script into a PSGI application without serving CGI scripts from a directory, to remove overhead of filesystem lookups, etc. perl v5.14.2 2011-11-02 Plack::App::CGIBin(3pm)
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