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Old 07-12-2013, 05:17 AM   #2
ThomasDOtto
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Location: Cambrdige, UK

Join Date: Mar 2012
Posts: 12
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Hi Akjones,

it is actually a bug in PAGIT, that will be fixed in the next version, sorry. The path in the promer file are not consistent with the installation.

Assuming you have sourced the configuration file of PAGIT, or working on the virtual machine, do
source nucmer
Looking into this file, like with less. Following should be seen:
use lib "$ENV{PAGIT_HOME}/lib";
use Foundation;
use File::Spec::Functions;
use strict;

my $AUX_BIN_DIR = "$ENV{PAGIT_HOME}/bin/aux_bin";
my $BIN_DIR = "$ENV{PAGIT_HOME}/bin";
my $SCRIPT_DIR = "$ENV{PAGIT_HOME}/bin/scripts";

If you do the same with promer, the variable are set absolutely, and not with
$ENV{PAGIT_HOME}/bin/

If you change promer to the same values than nucmer, it should work. Let me know if not, and I'll send you the fixed file, or put in on the pagit web page.

Cheers,
Thomas
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