[Bioperl-l] How to run hmmpfam

[Marc Logghe]

Hi Lixiao,

> MSG: Hmmpfam call (  -E 0.0001 myhmms 7LES_DROME) crashed: 0
> 
This error you typically get when bioperl is not able to find the path
to hmmpfam (just in front of '-E' you should see the path of the
executable, which is missing here).
There are several ways to do this:
1) PassEnv (or SetEnv) for HMMPFAMDIR in your apache configuration
2) set it directly in your cgi script:
$ENV{HMMPFAMDIR} = '/your/path/to/hmmfam_folder';
Important remark: in both cases HMMPFAMDIR should contain the path only,
e.g. /usr/local/bin, not including the name of the executable itself
(hmmpfam) !
3) pass the full path (this time including the executable) as a
parameter:
my $factory = Bio::Tools::Run::Hmmpfam->new(PROGRAM =>
'/usr/local/bin/hmmpfam');# or wherever your exe is located

HTH,
Marc