[maker-devel] Using GDBM_File instead of DB_File

[Carson Holt]

DB_File is being called by Bio::DB::Fasta.  I can check the object
returned when using GDBM_File instead to see if the index file names are
contained on the object, as I'm just assuming an extension of '.index'.
I'll look around to see if the extension name is assumed anywhere else.

Thanks,
Carson


On 12-05-31 8:34 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>Hello,
>
>I've been struggling for a few days to get maker up and running with MPI
>on a debian squeeze system. Compiling a new perl 5.16 exclusively for
>maker I wound down to that the segfaults came from DB_File. Even by
>recomiling and updating that module, nothing worked. After checking for
>dependencies on DB_File in maker, I concluded that the only dependency
>was through the GI::localize_file, which expects the FastaDB to be
>instantiated with DB_File. However, FastaDB can run on GDBM_File too. I
>patched the calls to GI::localize_file in maker to handle the .pag/.dir
>extensions used by GDBM (below). With this patch applied maker is running
>for me, even when I have deleted the DB_File module from the perl path
>and made sure that GDBM_File is installed. My basic question is if there
>is any other dependency for DB_File which I have missed which may break
>things?
>
>cheers,
>Mikael
>
>--- maker.orig	2012-03-30 15:48:05.000000000 +0200
>+++ maker	2012-05-31 10:35:30.253022648 +0200
>@@ -512,7 +515,12 @@
> }
> if($size > 1){
>     carp "Calling GI::localize_file" if($main::debug);
>-    GI::localize_file("$gdbfile.index");
>+    if( -f "$gdbfile.index.dir" ){
>+	GI::localize_file("$gdbfile.index.dir");
>+	GI::localize_file("$gdbfile.index.pag");
>+    }else{
>+    	GI::localize_file("$gdbfile.index");
>+    }
>     carp "Calling GI::localize_file" if($main::debug);
>     $gdbfile = GI::localize_file($gdbfile);
> }
>
>
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