[EMBOSS] Database access external app

[Peter Rice]

Stefanie Lager wrote:

> Marc,
> 
> I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
> and I try to retrive from a human genome database (each chr is a BIG
> fasta file). The formatdb indexing seems OK, fastacmd works on
> commandline. But I don't get any error from EMBOSS it just can't retrive
> entries (it just hangs there forever). 

The hang is a known problem to be fixed in 2.8.1 - entries over a 
certain size will hang in 2.8.0 because we added a wait loop to catch 
zombie processes.

As a quick fix (patch version of ajfile.c to be added to the FTP 
server), you can:

edit ajax/ajfile.c

in function ajFileNewInPipe, remove this loop at the end of the function:

     ret = -1;
     while(ret != pid)
     {
         ret = wait(&status);
         if(ret == -1)
             if(ret != EINTR)
                 ret = pid;
     }

Then make (and make install if you installed EMBOSS)

This loop will hang if the external process has unread data. (The real 
fix is to move this loop to the file close functions)

Hope this helps,

Peter Rice