Update ProphET_standalone.pl to use RealBin

[microbioticajon]

Hi Guys, thought I would make an issue for this PR: #37

Changed GFFLib import to look in the physical location of the ProphET_standalone.pl script using FindBin::RealBin. Currently the code uses FindBin::Bin which will not follow symbolic links if, for example, you symlink /opt/prophet/ProphET_standalone.pl to: /usr/local/bin/ProphET_standalone.pl

I have checked this change with ProphET_standalone.pl -h but not much further...

Cheers,
Jon

[microbioticajon]

Oddly, I think this might be related to: #38

[tseemann]

I use my $EXE = $FindBin::RealScript; all the time. It follows symlinks.

[microbioticajon]

I use my $EXE = $FindBin::RealScript; all the time. It follows symlinks.

Hi @tseemann, thanks for the reply!

You are correct FindBin::RealScrip will follow symlinks as you would expect. However, ProphET_standalone.pl uses FindBin::Bin not FindBin::RealBin. As such it wont find the shipped GFFLib as it is looking in a path relative to the symlink not the concrete file.

In ProphET_standalone.pl, change:

use lib "$FindBin::Bin/UTILS.dir/GFFLib";

to:

use lib "$FindBin::RealBin/UTILS.dir/GFFLib";

This way you dont need to add:
export PERL5LIB <Folder_you_installed_prophet>/UTILS.dir/GFFLib

For the purpose of others coming across this, the following docs explain the difference https://metacpan.org/pod/FindBin::Real

Bin

• path to bin directory from where script was invoked

RealBin

• Bin() with all links resolved

I hope this helps clarify my problem :)

[tseemann]

Yep - i use the same system in all my tools.

SRC
+- bin
    +- tool
+- perl5
    +- MyModule.pm

% head bin/tool

use FindBin;
use lib "$FindBin::RealBin/../perl5";
use MyModule;