Hi, All: Thank you for all your inputs. They really help me a lot~~~~~~[?] I downloaded the package "UnxUtils" and put my perl program under its "bin" folder. After I changed the windows system "path" variable, I can run the perl in the DOS system.
Only when I run the code below I have a little problem: *cat ids_overlap_* | sort -u > "a file name"* I have 3 files named as *ids_overlap_*(21Us/coding/ram)*. The error message is: *The system cannot find the file specified. cat.exe: write error : invalid argument* I wonder there is more than one version of "cat.exe or sort.exe" or the calling code (_*?) is not right? Again, thanks for all your inputs. Have a nice day! Fei On Wed, Aug 19, 2009 at 10:20 AM, Daniel Bara < [email protected]> wrote: > 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<http://www.math.utah.edu/%7Ebeebe/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<http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html>". > 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 > _______________________________________________ > Perl-Win32-Users mailing list > [email protected] > To unsubscribe: http://listserv.ActiveState.com/mailman/mysubs > > >
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