[Bioperl-l] Infernal parser

Chris Fields cjfields at illinois.edu
Mon Jul 5 12:18:30 EDT 2010


Marcela,

After taking a look again and running a few local checks, I found that setting INFERNALDIR does work after all.  I committed some code so that you can also explicitly set program_dir() as well, so the order of preference is:

setting program_dir() > INFERNALDIR > PATH

failing if an executable isn't found in any of those.  That shouldn't be necessary, though (setting INFERNALDIR in your local env should suffice).  Note that the Infernal wrapper only really supports Infernal 1.0 and up now, but the older releases still support pre-1.0 if you need them.

chris

On Jul 5, 2010, at 10:19 AM, Chris Fields wrote:

> Just looked at the code, it appears this is a bit inflexible; I had originally set it up so that you could define INFERNALDIR for this, but it appears this is never used.  I can work on adding this in.
> 
> chris
> 
> On Jul 5, 2010, at 7:57 AM, Marcela Davila wrote:
> 
>> Hi there!
>> 
>> I was wondering where I can set a different program directory (a local
>> directory that has a different version of the Infernal package) rather
>> than that specified in the ENV variable to run cmsearch while using
>> Bio::Tools::Run::Infernal.
>> 
>> Thanks!
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> 
> 
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