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Full Discussion: Batch file and perl
Special Forums Windows & DOS: Issues & Discussions Batch file and perl Post 302926933 by ongoto on Friday 28th of November 2014 04:25:13 PM
Old 11-28-2014
You're going about this all wrong. Smilie
The files you have attached
  • windows_annovar.sh
  • windows_annovar.pl
are the same file. You can't just rename files and expect them to run with different interpreters.

Code:
Line 117  windows_annovar.sh

    cd 'C:\Users\cmccabe\Desktop\annovar'
              $( perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver ... blah blah blah)

This is calling perl table_annovar.pl to access a database (humandb) I think. Do you have all those perl files installed?? If so, perl needs to know where to find them. The full path to the folder that contains them should be in PATH as well as the full path to the perl modules.

PATH belongs in windows_annovar.sh...not this one. Actually, it belongs in the shell environment.
Get rid of this file.
Code:
windows_annovar.pl
#!/bin/bash

PATH="C:\\cygwin\\bin\perl.exe:${PATH}"
...
...


Last edited by ongoto; 11-28-2014 at 05:31 PM..
 

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FindBin(3perl)						 Perl Programmers Reference Guide					    FindBin(3perl)

NAME
FindBin - Locate directory of original perl script SYNOPSIS
use FindBin; use lib "$FindBin::Bin/../lib"; or use FindBin qw($Bin); use lib "$Bin/../lib"; DESCRIPTION
Locates the full path to the script bin directory to allow the use of paths relative to the bin directory. This allows a user to setup a directory tree for some software with directories "<root>/bin" and "<root>/lib", and then the above example will allow the use of modules in the lib directory without knowing where the software tree is installed. If perl is invoked using the -e option or the perl script is read from "STDIN" then FindBin sets both $Bin and $RealBin to the current directory. EXPORTABLE VARIABLES
$Bin - path to bin directory from where script was invoked $Script - basename of script from which perl was invoked $RealBin - $Bin with all links resolved $RealScript - $Script with all links resolved KNOWN ISSUES
If there are two modules using "FindBin" from different directories under the same interpreter, this won't work. Since "FindBin" uses a "BEGIN" block, it'll be executed only once, and only the first caller will get it right. This is a problem under mod_perl and other persistent Perl environments, where you shouldn't use this module. Which also means that you should avoid using "FindBin" in modules that you plan to put on CPAN. To make sure that "FindBin" will work is to call the "again" function: use FindBin; FindBin::again(); # or FindBin->again; In former versions of FindBin there was no "again" function. The workaround was to force the "BEGIN" block to be executed again: delete $INC{'FindBin.pm'}; require FindBin; KNOWN BUGS
If perl is invoked as perl filename and filename does not have executable rights and a program called filename exists in the users $ENV{PATH} which satisfies both -x and -T then FindBin assumes that it was invoked via the $ENV{PATH}. Workaround is to invoke perl as perl ./filename AUTHORS
FindBin is supported as part of the core perl distribution. Please send bug reports to <perlbug@perl.org> using the perlbug program included with perl. Graham Barr <gbarr@pobox.com> Nick Ing-Simmons <nik@tiuk.ti.com> COPYRIGHT
Copyright (c) 1995 Graham Barr & Nick Ing-Simmons. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2011-09-26 FindBin(3perl)
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