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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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CPANPLUS::Internals::Utils(3perl)			 Perl Programmers Reference Guide			 CPANPLUS::Internals::Utils(3perl)

NAME
CPANPLUS::Internals::Utils - convenience functions for CPANPLUS SYNOPSIS
my $bool = $cb->_mkdir( dir => 'blah' ); my $bool = $cb->_chdir( dir => 'blah' ); my $bool = $cb->_rmdir( dir => 'blah' ); my $bool = $cb->_move( from => '/some/file', to => '/other/file' ); my $bool = $cb->_move( from => '/some/dir', to => '/other/dir' ); my $cont = $cb->_get_file_contents( file => '/path/to/file' ); my $version = $cb->_perl_version( perl => $^X ); DESCRIPTION
"CPANPLUS::Internals::Utils" holds a few convenience functions for CPANPLUS libraries. METHODS
$cb->_mkdir( dir => '/some/dir' ) "_mkdir" creates a full path to a directory. Returns true on success, false on failure. $cb->_chdir( dir => '/some/dir' ) "_chdir" changes directory to a dir. Returns true on success, false on failure. $cb->_rmdir( dir => '/some/dir' ); Removes a directory completely, even if it is non-empty. Returns true on success, false on failure. $cb->_perl_version ( perl => 'some/perl/binary' ); "_perl_version" returns the version of a certain perl binary. It does this by actually running a command. Returns the perl version on success and false on failure. $cb->_version_to_number( version => $version ); Returns a proper module version, or '0.0' if none was available. $cb->_whoami Returns the name of the subroutine you're currently in. _get_file_contents( file => $file ); Returns the contents of a file $cb->_move( from => $file|$dir, to => $target ); Moves a file or directory to the target. Returns true on success, false on failure. $cb->_copy( from => $file|$dir, to => $target ); Moves a file or directory to the target. Returns true on success, false on failure. $cb->_mode_plus_w( file => '/path/to/file' ); Sets the +w bit for the file. Returns true on success, false on failure. $uri = $cb->_host_to_uri( scheme => SCHEME, host => HOST, path => PATH ); Turns a CPANPLUS::Config style "host" entry into an URI string. Returns the uri on success, and false on failure $cb->_vcmp( VERSION, VERSION ); Normalizes the versions passed and does a '<=>' on them, returning the result. $cb->_home_dir Returns the user's homedir, or "cwd" if it could not be found $path = $cb->_safe_path( path => $path ); Returns a path that's safe to us on Win32 and VMS. Only cleans up the path on Win32 if the path exists. On VMS, it encodes dots to _ using "VMS::Filespec::vmsify" ($pkg, $version, $ext) = $cb->_split_package_string( package => PACKAGE_STRING ); Splits the name of a CPAN package string up into its package, version and extension parts. For example, "Foo-Bar-1.2.tar.gz" would return the following parts: Package: Foo-Bar Version: 1.2 Extension: tar.gz perl v5.14.2 2014-09-29 CPANPLUS::Internals::Utils(3perl)
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