Greetings! I'll be honest and say that it sounds like you've made this problem overly complex. Can you please provide a link to the module you're trying to install? That way people can better advise. If you have not already done so please read and understand PerlMonks for the Absolute Beginner.

Update: typo

Thanks for the quick reply ^^

 
"it sounds like you've made this problem overly complex" I probably have, but this is the result of reading tutorials on the web... everyone seems to assume that I want to install CPAN packages... 
 
Here is the download link: http://www.mybiosoftware.com/protein-sequence-analysis/11826 
 
Beware, someone in my institute who knows a bit of Perl told me it is not the most elegantly written script he has ever seen...

This script requires the BioPerl suite of modules. I'm running Strawberry Perl 5.18.2 on Windows 7 64bit, DWIM perl ships with Strawberry 5.14, which isn't anything to worry about. To install BioPerl open a command prompt and type the following:

cpan BioPerl
[download]

This will download, unpack and build the distribution and it's dependencies automatically. This may take some time. I skipped the online tests (they'd fail from my work laptop due to network issues). After this you can run the software you linked to by unpacking the download and just running the script:

C:\datasetConstructor>perl pepFly.pl
Input File>
# of output files>
[download]

Let me know if you have any problems. Note that I'm not a Bioinformatician. See also Tutorials->Perl and Bioinformatics.

Update: fixed typo.

Arthfael:

Ugh! It looks like someone round-tripped the McCarthy-SourceData.txt file through Excel. The ninth column looks as if it's been munged (12/18 being turned into 18-Dec, etc.).

...roboticus

When your only tool is a hammer, all problems look like your thumb.

In general, you don't necessarily have to install .pm files (or even their associated .dll files, if any) to be able to run scripts), Perl just has to be able to find them.

In my experience, most scripts that come with .pm files are able to locate their "private" .pm files on their one, as long as you either unzip/unpack them, then run the script from that location, or you put the .pm files (and .dll files, if any) in the same folder as the script.

OK, thanks guys.

I checked and indeed I had not installed BioPerl. However, even after installing it the output is unchanged: I get files with the headers I would be expecting to get based on the associated publication, but no content under the headers.

About the Excel-corrupted file: I have made a fixed version. I will never understand why Microsoft does not want to fix this. It's so annoying when protein Sep7 randomly turns into September 7!

Hi monks,

Sorry to bother you guys again but my issue hasn't been resolved. I have checked and while all the necessary packages are now installed, the script still only produces empty headers as output. I have tried contacting the script maker but since it dates from 2007 he may not reply. Any idea why the script is failing?