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Full Discussion: Bash menu not running
Top Forums Programming Open Source Bash menu not running Post 302939676 by cmccabe on Friday 27th of March 2015 02:53:44 PM
Old 03-27-2015
The hope was to store the output directory as a variable ($FILENAME) but I don't think that is the right way to do it. I changed the code to the below and put the .pl in the annovar directory to make it easier.

The overall goal is use ${id}.txt.hg19_multianno.txt as the input file and after the perl script is run on that file the output file is saved to the path L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_${id}.txt . Thank you Smilie.

Code:
matrix() {
    
     cd 'C:\Users\cmccabe\Desktop\annovar'
     $( perl -ne 'chomp; system ("perl matrix.pl < ${id}.txt.hg19_multianno.txt" )' >> L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_${id}.txt
	 
	 printf "Process complete and new file saved in, Are there additional target gene patients? Y/N "; read match_choice
	 case "$match_choice" in
	    [yY]) id=""; menu ;;
        [nN]) id=""; printf "\n Goodbye! /n/n "; sleep 2 && exit ;;
		esac
}

 

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Mojo::Command(3pm)					User Contributed Perl Documentation					Mojo::Command(3pm)

NAME
Mojo::Command - Command base class SYNOPSIS
# Lower case command name package Mojolicious::Command::mycommand; # Subclass use Mojo::Base 'Mojo::Command'; # Take care of command line options use Getopt::Long 'GetOptions'; # Short description has description => "My first Mojo command. "; # Short usage message has usage => <<"EOF"; usage: $0 mycommand [OPTIONS] These options are available: -s, --something Does something. EOF # <suitable Futurama quote here> sub run { my $self = shift; # Handle options local @ARGV = @_; GetOptions('s|something' => sub { $something = 1 }); # Magic here! :) } DESCRIPTION
Mojo::Command is an abstract base class for Mojo commands. See Mojolicious::Commands for a list of commands that are available by default. ATTRIBUTES
Mojo::Command implements the following attributes. "description" my $description = $command->description; $command = $command->description('Foo!'); Short description of command, used for the command list. "quiet" my $quiet = $command->quiet; $command = $command->quiet(1); Limited command output. "usage" my $usage = $command->usage; $command = $command->usage('Foo!'); Usage information for command, used for the help screen. METHODS
Mojo::Command inherits all methods from Mojo::Base and implements the following new ones. "app" my $app = $command->app; Currently active application. # Introspect say "Template path: $_" for @{$command->app->renderer->paths}; "chmod_file" $command = $command->chmod_file('/home/sri/foo.txt', 0644); Portably change mode of a file. "chmod_rel_file" $command = $command->chmod_rel_file('foo/foo.txt', 0644); Portably change mode of a file relative to the current working directory. "class_to_file" my $file = $command->class_to_file('Foo::Bar'); Convert a class name to a file. Foo::Bar -> foo_bar FOO::Bar -> foobar FooBar -> foo_bar FOOBar -> foobar "class_to_path" my $path = $command->class_to_path('Foo::Bar'); Convert class name to path. Foo::Bar -> Foo/Bar.pm "create_dir" $command = $command->create_dir('/home/sri/foo/bar'); Portably create a directory. "create_rel_dir" $command = $command->create_rel_dir('foo/bar/baz'); Portably create a directory relative to the current working directory. "get_all_data" my $all = $command->get_all_data; my $all = $command->get_all_data('Some::Class'); Extract all embedded files from the "DATA" section of a class. "get_data" my $data = $command->get_data('foo_bar'); my $data = $command->get_data('foo_bar', 'Some::Class'); Extract embedded file from the "DATA" section of a class. "help" $command->help; Print usage information for command. "rel_dir" my $path = $command->rel_dir('foo/bar'); Portably generate an absolute path for a directory relative to the current working directory. "rel_file" my $path = $command->rel_file('foo/bar.txt'); Portably generate an absolute path for a file relative to the current working directory. "render_data" my $data = $command->render_data('foo_bar', @args); Render a template from the "DATA" section of the command class. "render_to_file" $command = $command->render_to_file('foo_bar', '/home/sri/foo.txt'); Render a template from the "DATA" section of the command class to a file. "render_to_rel_file" $command = $command->render_to_rel_file('foo_bar', 'foo/bar.txt'); Portably render a template from the "DATA" section of the command class to a file relative to the current working directory. "run" $command->run; $command->run(@ARGV); Run command. Meant to be overloaded in a subclass. "write_file" $command = $command->write_file('/home/sri/foo.txt', 'Hello World!'); Portably write text to a file. "write_rel_file" $command = $command->write_rel_file('foo/bar.txt', 'Hello World!'); Portably write text to a file relative to the current working directory. SEE ALSO
Mojolicious, Mojolicious::Guides, <http://mojolicio.us>. perl v5.14.2 2012-09-05 Mojo::Command(3pm)
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