Re: StandAloneBlast.pm, bl2seq() and tempfiles on Win32/cygwin

It's not StandALoneBlast's fault: it's using Bio::Root::IO::tempfile() 
which uses some convoluted logic that I can't follow (and, if I 
remember right, is a copy of an older File::Temp incarnation).

So, folks, how can we best inform BioPerl where we want it to make 
temporary files?

-Aaron

On Feb 24, 2004, at 11:11 AM, Brian Osborne wrote:

> Aaron,
>
> That could work. Unfortunately that would mess up the path for those
> applications that DO use Unix-style paths.
>
> Well, hold on, let me try....
>
> No, neither worked:
>
> MSG: Could not open /tmp/Av0MhgqzIJ: No such file or directory
>
> StandAloneBlast seems not to care about either env's. That's not nice.
>
>
> Brian O.
>
> -----Original Message-----
> From: Aaron J. Mackey [mailto:amackey@xxxxxxxxxxxxxx]
> Sent: Tuesday, February 24, 2004 10:58 AM
> To: Brian Osborne
> Subject: Re: [Bioperl-l] StandAloneBlast.pm, bl2seq() and tempfiles on
> Win32/cygwin
>
> Ahh, right; perhaps the $TEMPDIR (or $TEMP?) environment variable would
> do the trick?
>
> -Aaron
>
> On Feb 24, 2004, at 10:46 AM, Brian Osborne wrote:
>
> > Aaron,
> >
> > Or ask the author for a way to set the tempdir, in my case it would be
> > "e:/cygwin/tmp". I couldn't see such a thing in the documentation,
> > perhaps I
> > missed it though.
> >
> > BIO
> >
> > -----Original Message-----
> > From: Aaron J. Mackey [mailto:amackey@xxxxxxxxxxxxxx]
> > Sent: Tuesday, February 24, 2004 10:32 AM
> > To: Brian Osborne
> > Subject: Re: [Bioperl-l] StandAloneBlast.pm, bl2seq() and tempfiles on
> > Win32/cygwin
> >
> > Ooo, that's probably it; what's the solution?
> >
> > -Aaron
> >
> > On Feb 24, 2004, at 10:22 AM, Brian Osborne wrote:
> >
> > > Aaron,
> > >
> > > Because he's using the BLAST Win binaries which don't understand
> > > Cygwin
> > > paths?
> > >
> > > Meaning these work:
> > >
> > > blastall -i test.fa -d testdb.fa -p blastn
> > >
> > > blastall -i e:/cygwin/home/bosborne/test.fa -d test.fa -p blastn
> > >
> > >
> > > But this doesn't:
> > >
> > > blastall -i /home/bosborne/test.fa -d test.fa -p blastn
> > >
> > > ?
> > >
> > >
> > > Brian O.
> > >
> > > -----Original Message-----
> > > From: bioperl-l-bounces@xxxxxxxxxxxxxxxxxxx
> > > [mailto:bioperl-l-bounces@xxxxxxxxxxxxxxxxxxx]On Behalf Of Aaron J.
> > > Mackey
> > > Sent: Monday, February 23, 2004 4:11 PM
> > > To: Bioperl list
> > > Cc: Sushma Parankush Das
> > > Subject: [Bioperl-l] StandAloneBlast.pm,bl2seq() and tempfiles on
> > > Win32/cygwin
> > >
> > >
> > > A colleague of mine is frustrated by attempting to use
> > > Bio::Tools::Run::StandAloneBlast to run bl2seq (Perl 5.8.2, bioperl
> > > 1.4, windows XP, CygWin, etc.):
> > >
> > > # synopsis:
> > > $seq1 = $seqio->next_seq;
> > > $seq2 = $seqio->next_seq;
> > > $factory->bl2seq($seq1, $seq2);
> > >
> > > StandAloneBlast successfully writes two temp files in /tmp, which 
> > > have
> > > the sequence data and can be read by "less" or "cat" in another open
> > > window (with the main program suspended in debugger); however, if
> > > either the program code or I at the command line attempt to run
> > > bl2seq,
> > > it dies with "Cannot open file /tmp/7aasd78asd".  If I "cp" the temp
> > > files into new files, it runs fine.  Or, if I call
> > > $factory->bl2seq($file1, $file2) with filenames instead of seq
> > > objects,
> > > it also works fine.  I have tried various incarnations of closing the
> > > filehandles and Bio::SeqIO objects that StandAloneBlast.pm is using 
> > > to
> > > generate these temp files, but to no avail (and of course, the
> > > tempfiles disappear upon program completion).
> > >
> > > This is not the "failed to open tempfile; too many files open" error
> > > seen previously, and I also expect a fair number of "works for me"
> > > responses - please save your breath.
> > >
> > > Thanks for any input,
> > >
> > > -Aaron
> > >
> > > _______________________________________________
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> > >
> > >
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