Dear monks, Obviously, I still have a lot to learn on perl. Here is my latest prob: I wrote some code in perl using the bioperl modules. Everything went fine! Now I changed some of the script (added some cgi lines and stuff), to make it accessible for a web service. Basically, the user enters some input data (dna sequences) and the perl script returns an output analysis. However, it seems that I have a prob with the temporary directory, because on the server error log, I get error messages saying this: 
align' is not recognized as an internal or external command, operable 
+program or batch file.

-------------------- WARNING ---------------------
MSG: Clustalw call ( align  -infile=\\tmp\\WPGAS2NLA8\\jHRbMLTo05 -out
+put=gcg   -ktuple=2 -matrix=BLOSUM -outfile=\\tmp\\WPGAS2NLA8\\XTFEoZ
+HFGV) crashed: 256
---------------------------------------------------, 
Can't call method "uniq_seq" on an undefined value at C:/perl/site/lib
+/transposonTool.pm line 67, <GEN0> line 4.,

[download]
Now on the documentation of Bio::Tools::Run::Alignment::Clustalw, it is said that this type of error occurs when the input directory or input file is wrong... Like I said before the script works perfect when I use it "offline". Is it possible that when my script is called from a web form, the tmp dir is somehow different than what it is normally? Is there anyway around it? Can I change something in the httpd.conf file ? I don't know what to try anymore... Julio

In reply to perl - apache - winxp tmp dir??? by julio_514

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