09-18-2011
It is your PATH variable...why dont you copy the PATH from the terminal into the script instead of initializing it to dirs that dont contain those commands...clustal seqret collapse1.5
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Env(3pm) Perl Programmers Reference Guide Env(3pm)
NAME
Env - perl module that imports environment variables as scalars or arrays
SYNOPSIS
use Env;
use Env qw(PATH HOME TERM);
use Env qw($SHELL @LD_LIBRARY_PATH);
DESCRIPTION
Perl maintains environment variables in a special hash named %ENV. For when this access method is inconvenient, the Perl module "Env"
allows environment variables to be treated as scalar or array variables.
The "Env::import()" function ties environment variables with suitable names to global Perl variables with the same names. By default it
ties all existing environment variables ("keys %ENV") to scalars. If the "import" function receives arguments, it takes them to be a list
of variables to tie; it's okay if they don't yet exist. The scalar type prefix '$' is inferred for any element of this list not prefixed by
'$' or '@'. Arrays are implemented in terms of "split" and "join", using $Config::Config{path_sep} as the delimiter.
After an environment variable is tied, merely use it like a normal variable. You may access its value
@path = split(/:/, $PATH);
print join("
", @LD_LIBRARY_PATH), "
";
or modify it
$PATH .= ":.";
push @LD_LIBRARY_PATH, $dir;
however you'd like. Bear in mind, however, that each access to a tied array variable requires splitting the environment variable's string
anew.
The code:
use Env qw(@PATH);
push @PATH, '.';
is equivalent to:
use Env qw(PATH);
$PATH .= ":.";
except that if $ENV{PATH} started out empty, the second approach leaves it with the (odd) value "":."", but the first approach leaves it
with ""."".
To remove a tied environment variable from the environment, assign it the undefined value
undef $PATH;
undef @LD_LIBRARY_PATH;
LIMITATIONS
On VMS systems, arrays tied to environment variables are read-only. Attempting to change anything will cause a warning.
AUTHOR
Chip Salzenberg <chip@fin.uucp> and Gregor N. Purdy <gregor@focusresearch.com>
perl v5.16.2 2012-10-11 Env(3pm)