[Bioperl-l] StandAloneBlast and tempfiles

Peter Kos kos@rite.or.jp" <kos@rite.or.jp
Tue, 19 Mar 2002 17:53:13 +0900


> The environment variable TMPDIR or TEMPDIR should set it for you- 
this may
> depend on whether or not you have File::Temp installed...  I can't
> remember where the precedence order gets set.  I think File::Temp 
> look for TMPDIR then TEMPDIR then use /tmp.  Can I get you to try 
out this
> and report back?  I'm sorry that the exe wrappers are not doing the 
> job they could wrt to tempfile stuff - my hope is the next round of
> implementation of the bioperl-pipeline will migrate the runnables 
into a
> new system that will be a little more unified and easier to fix 
> types of problems globally.
Thanx. Sure.
File::Temp is installed.
TEMPDIR does not seem to have any effect (on my machine). That's what 
I already figured out by myself and that's when I gave up and wrote 
some lines to "manually" remove the tempfiles.
However TMPDIR works fine.

local $ENV{"TMPDIR"}= /someplace/;

does not work, it may not be a problem. Having two different TMPDIRs 
in two separate shells does not seem to conflict, I think. I just 
need to make sure that each time I run StandAloneBlast I set the 
TMPDIR if I care where it is. So it is perfect, thank you very much.

> > =offtopic Could someone help me out, how to set the buffer of the 
command line in
> > tcsh/Solaris?

> I *think* you can use the find command instead of ls to get this
> same information and won't have the same limitation.
> find /tmp -name "*" | xargs rm
It may help. Now I tried this construct and it worked sofar. Not 
tested thoroughly though. It again circumvents my problem, rather 
than solves that, but it is surely faster to write than a some-lines 
perl script, so thank you for the good idea.

I just thought that lots of folks on this list may do similar bulk 
sequencing as I do and may have many thousands of files per 
directories and they may know the way using 'ls' and such.

Thank you again