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"
Re: Getting started with BioPerl on Windows 8.1 64-bit
by Discipulus (Canon) on Feb 27, 2015 at 08:31 UTC
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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
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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
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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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