Hi Fei,
I had the same problem some time ago.
I solved it with tools from the following resource.
http://www.math.utah.edu/~beebe/gnu-on-windows.html
Many DOS commands are different in UNIX. Like dir / ls or del rm.
The other issue you will have to consider when modifying the script is
how you move/direct to directories.
I do not remember exactly but in some cases in windows // were
necessary.
I finally moved to Mac
Hope it helps.
Daniel
On Aug 18, 2009, at 5:39 PM, Fei Shi wrote:
Hi, Dear perl experts:
I am a new hand of perl. I use perl because I am trying to
use a package called "miRDeep". I install the activeperl 5.10 for
windows. Then I used the MS DOS to try perl.
But there is an error coming out when I tried to run this
command their demo: "perl auto_blast.pl 454_aligned.fa precursors.
fa-b > signatures".
The error message is as follows:
Copying subject file 'cp' is not recognized as an internal or
external command, operable program or batch file.
formatting subject file [NULL_Caption] ERROR: Could not open
blast_dir_temp/file_subject
Blasting query file against subject file
[NULL_Caption] WARNING: readdb: wrong version of formatdb was used
to make database blast_dir_temp/file_subject.
[NULL_Caption] WARNING: bartel_100023_x1: readdb: wrong version of
formatdb was used to make database blast_dir_temp/file_subject.
Parsing blast output:
'cat' is not recognized as an internal or external command,
operable program or batch file.
'cat' is not recognized as an internal or external command,
operable program or batch file.
'cat' is not recognized as an internal or external command,
operable program or batch file.
'rm' is not recognized as an internal or external command,
operable program or batch file.
'rm' is not recognized as an internal or external command,
operable program or batch file.
But I think the perl code "auto_blast.pl" is tested maturely by the
author of the package so I am suspicious that there may be something
wrong with my system?
The MS DOS is 5.1.2600 by windows XP. I wonder if the above error
message due to this or other reasons? I really appreciate if someone
can point me out of this and give me a clue of the problem.
Thank you very much for your time.
Sincerely,
Fei
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