On Tuesday 25 August 2009 01:27:52 Martyn Winn wrote:
>
> You should be able to do this kind of scripting.
>
> The CCP4 library will try to add an extension, iff there is not one
> already. But if you have set $tempfile to "foo.pdb" then it shouldn't
> add anything.
Since several people have expressed confusion at why this is a problem,
let me expand a little. I have a shell script that works fine
from the command line. Stripped to its essence, it looks like this:
#/bin/bash
#script tls2anisou
/usr/local/bin/tlsextract XYZIN $1 TLSOUT $1.tls
/usr/local/bin/tlsanl XYZIN $1 TLSIN $1.tls XYZOUT $1_bcor.pdb << EOF
BRESID true
ISOOUT full
END
EOF
So from the command line I can type
tls2anisou myfile.pdb
and all is well.
But now I want to run the script from a cgi script as part of the
processing by a web service. No matter what the name of the file
that was originally uploaded, the web server has homogenized it to
a local temporary file whose name is generated by a hash function
from the pid. The cgi script passes this arbitrary file name to
the script in $1, but of course at this point it does not end in
".pdb" and in fact has no extension at all.
My current work-around is the following variant:
#/bin/bash
#
# This script is designed to be called from inside a cgi script,
# so its environment has been stripped. We need to add back a
# minimal set of environmental variables in order to run CCP4 programs.
#
export CCP4_SCR=/var/www/webtmp
export CLIBD=/dev/null
export CINCL=/var/www/local/include
#
# I have no idea why this is necessary, but the CCP4 programs below
# seem to add a ".brk" on the end of XYZIN filenames
mv $1 $1.brk
#
/usr/local/bin/tlsextract XYZIN $1 TLSOUT $1.tls
/usr/local/bin/tlsanl XYZIN $1 TLSIN $1.tls XYZOUT $1_bcor.pdb << EOF
BRESID true
ISOOUT full
END
EOF
That works, but at the cost of an unnecessary file copy operation.
I was hoping I could set something in $CINCL/environ.def that would
fix the naming problem, but if so I haven't figured it out yet.
> Code is in ccp4_general.c if you want to sabotage it ...
Thanks. I might do that.
> The list of default extensions is in $CCP4/include/environ.def
> (but we obviously need to update .brk to .pdb)
Yeah, I saw that. That lets you change the default extension,
but based on my blind experimentation it doesn't let you remove
the extension altogether. Perhaps I didn't try the right thing?
Given the hint to look in ccp4_general.c, I may be able to fix that.
thanks,
Ethan
>
> HTH
> Martyn
>
> On Mon, 2009-08-24 at 17:30 -0700, Ethan Merritt wrote:
> > Not sure this is the right place to ask, but...
> >
> > I'm trying to chain some ccp4 programs together via a script.
> > It creates temporary files with arbitrary names based on the process id.
> > The problem is that when I try to pass one of these files to the
> > next program in the chain, as in:
> >
> > tlsanl XYZIN $tempfile <<EOF
> > ...
> > EOF
> >
> > The ccp4 libraries seem to expand this to be an input file named
> > $tempfile.brk
> >
> > Is there any way to make the programs _not_ append a useless extension
> > ".brk" in a scripted environment?
> >
> --
> ***********************************************************************
> * *
> * Dr. Martyn Winn *
> * *
> * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
> * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk *
> * Fax: +44 1925 603825 Skype name: martyn.winn *
> * URL: http://www.ccp4.ac.uk/martyn/ *
> ***********************************************************************
>
>
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
