Re: [Condor-users] wu-blast

[Zachary Miller <zmiller@xxxxxxxxxxx>]

On Tue, Aug 26, 2008 at 11:30:01AM -0600, Gary Orser wrote:
> Hi all,
> 
> Having a really dumb problem, and wondered if anyone else had solved
> it.
> 
> Trying to use wu blastp and am getting this error.
> 
> FATAL:  Invalid program name:  condor_exec.exe.  This is the unified BLASTA
>         program from the WU BLAST package (see http://blast.wustl.edu).  It is
>         not intended to be invoked by this name.  Instead, make soft links to
>         it with the UNIX "ln" command, to produce names that contain the
>         strings "blastp", "blastn", "blastx", "tblastn" and "tblastx" anywhere
>         within them.  Alphabetic case is unimportant.  See the UNIX man
>         (manual) page for the "ln" command for more information on creating
>         soft links (the -s option).  Hard links can also be made by omitting
>         -s, but they may be more difficult to manage.EXIT CODE 28
> 
> Looks like blastp has to be the first command line argument, and it's
> not under condor.
> 
> Anybody have a workaround?

the blast executable looks at the name of the executable to decide how it
should behave.  you can make this work, you just need to do the following:

1) make a wrapper script that invokes blast.  call it blastp_wrapper
	#!/bin/sh

	./blastp $@

2) modify your condor submit file by making the executable the wrapper script
   and then adding the real executable to the transfer_input_files.  (if you
   are not using file transfer, skip this and see below):

	executable = blastp_wrapper
	transfer_input_files = /path/to/real/blastp, whatever, was, here, before

that should do it.


if you are not using file transfer (you must be using a shared filesystem
like NFS or some such?), you'll still need to use a wrapper script, but you
don't need to transfer the executable.  just create the wrapper script and
call it blast_wrapper:
	#!/bin/sh

	/full/path/to/blastp @$

and then in your submit file change the executable to:
	executable = /full/path/to/blast_wrapper


let me know if you still have trouble.


cheers,
-zach