bls61793 has asked for the wisdom of the Perl Monks concerning the following question:

So, I need some help. I've been working on a project for a bit using several BioPerl Modules, and I'm having a hard time getting them set up and installed. I started with an Activestate install of Perl, and installed CPAN. However, the problem I was having is that I have a few required Perl modules that I was unable to install with CPAN, including Bio::Seq. CPAN told me two things: #1 I was missing two dependencies, including Data::Stag. and #2 dmake kept failing to execute (likely it didn't exist on my system). I tried to install the dependencies that I was missing, but I kept getting the same installation errors as #2. Because of this I came to the Monastery where someone suggested trying Citrus Perl instead of ActiveState, which I am now trying. I have downloaded and setup citrus perl such that I can us citrussterm.bat, but I'm honestly lost at this point. I would like to try and remove my previous (ActiveState) installation of perl and start over with CitrusPerl and get the modules I need installed. I'd really appreciate any help with this that I can get. Thanks a ton, -A Noob with a keyboard. Update: Now when I run CPAN.bat to launch cpan from the CitrusPerl directory and try to install the modules I need I keep getting the following error: "Could not make: unknown error"
  • Comment on Getting started with BioPerl on Windows 8.1 64-bit

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Re: Getting started with BioPerl on Windows 8.1 64-bit
by Discipulus (Canon) on Feb 27, 2015 at 08:31 UTC
    Based on my experience you need to switch to StrawberryPerl, no citrus, as the latter is destinated mainly to GUI developpers that want to use wxWidgets. I guess is not your case.
    Strawberry Perl is full functioning Perl distro with many useful accessories: you'll get a something very near to a standard Perl installation as on Linux, and you can use cpan or cpanp client to get modules because Strawberry Perl will includes all compilers you need for this. I suggest you the portable edition, but investigate a little on your own.

    So first you have to remove previous Perl installation (normal control panel -> remove program) then get your strawberry Perl an spend some boring time installing all modules you need using one of the several CPAN client available.

    HtH
    L*
    There are no rules, there are no thumbs..
    Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.
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Re: Getting started with BioPerl on Windows 8.1 64-bit
by CoVAX (Beadle) on Feb 27, 2015 at 07:41 UTC

    ActiveState supplies their Perl Package Manager (ppm) -- try running it to install the modules.

    E.g. (not tested):

    C:\Perl>ppm install BioPerl::SomeModule

    Enter "ppm help" to learn more about ppm

    There's also a GUI version:

    C:\Perl>ppm gui

    Searched for donut and crumpit. Found donate and stumbit instead.
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Re: Getting started with BioPerl on Windows 8.1 64-bit
by dasgar (Priest) on Feb 27, 2015 at 17:20 UTC

    If you want to install modules that need to be compiled (such as XS modules) in ActiveState's ActivePerl, you'll need to install MinGW and dmake from ActiveState's PPM repository. For 32-bit ActivePerl, that's all that you need to do. If you're using 64-bit ActivePerl, there may be additional steps needed, but that's outside the scope of my knowledge and experience.

    I'd agree with Discipulus' recommendation about using Strawberry Perl, which comes with the compiler and tools needed to install most of the modules from CPAN. (Some modules won't install on Windows due to OS dependencies.)

    Since I personally have not used it myself, I can't comment on Citrus Perl. Like you, I have seen a number of folks recommend it here at this site.

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      Thanks to both of you guys for recommending Strawberry Perl, I think I'm going to try that. I'll report back here with what I find, but hopefully that will work out for me.
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        So, I got Strawberry Perl installed on my windows machine, and was able to download my needed modules with no problem. So it seems to have worked. Thanks a lot guys!
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