[Bioperl-l] StandAloneBlast and tempfiles

[Jason Stajich]

On Sat, 16 Mar 2002, Peter Kos, PhD wrote:

> Hi,
>
> the StandAloneBlast swiftly and smoothly filled the file system of
> /tmp/ at the first overnight run. I've already figured out how it
> happened, so I inserted a small code at the end of each cycle (of many
> local Blasts)  which now deletes the temporary files, which in fact
> were not really temporary. Now I am happy to see that it is going to
> be fixed within the module, so others will not have this problem. I
> have some questions, however. 1., I could not figure out how to SET
> the $TEMPDIR. It would be nice to try whether the program speeds up a
> bit if I place the $TEMPDIR in another physical volume, not messing

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 will
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 best
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 these
types of problems globally.

> with the op.system. Furthermore, this way I could run more than one
> instances of this script without limitations. 2., =offtopic Could
> someone help me out, how to set the buffer of the command line in
> tcsh/Solaris? (Or how else to circumvent this:) (Or whom to ask) I am
> really sick of these error messages like: "/bin/ls: Arg list too long"
> after >ls -1 *.scf > fofn or simply >rm /tmp/* It was really fun
> writing the first couple of perl script aliases for built-in UNIX
> commands, but now it is enough. I admit that I have more than many
> files, but that's why I do not use a Commodore64. =cut
>
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


> Your help would really be highly appreciated
>
> Peter
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu