linear genome visualization

Question

[popayekid55]

Hi

I have installed all the dependency package for alitv as per the github instruction. I want to create image for custom genomes. I have made yml file as per the tutorials. I am getting following error

FATAL - Unable to load alignment module 'AliTV::Alignment::lastz' at /data/ngs/programs/AliTV-perl-interface/bin/../lib/AliTV/Script.pm line 123.

Googling didn't help. anyone who has used it please let me know how to fix the error. Or any other tools which generates similar image? Mauve/ contiguator / synmap apart from these.

Answer 1

[Philipp Bayer]

Normally AliTV should pick up its own Perl packages, strange.

You can manually add other modules like this:

 export PERL5LIB=/data/ngs/programs/AliTV-perl-interface/lib/AliTV/Alignment:$PERL5LIB

That will tell Perl where the missing lastz.pm is. It may then complain about other missing modules in other directories, you can amend the PERL5LIB environment variable to include those folders too.

Edit: I'm still a bit baffled why this does not work for you, these two lines in alitv.pl should add those libraries:

use FindBin::Real;
use lib FindBin::Real::Bin() . '/../lib';

Maybe on your system the main binary is located somewhere else so that it cannot find a lib folder one folder up...